cover

pip install pdb-profiling

Load Modules

In [1]:
from tqdm import tqdm

from pdb_profiling import default_config

your_output_folder = "C:/GitWorks/pdb-profiling/test/demo"

default_config(your_output_folder)
In [2]:
from pdb_profiling.processors import SIFTS, SIFTSs, PDB, PDBs
from pdb_profiling.utils import DisplayPDB
In [3]:
SIFTS.chain_filter, SIFTS.entry_filter = '', ''

Some knowledge you should know beforehand

Demo UniProt

In [4]:
demo = SIFTS('P21359')

Monomeric Protein

  • pdb_id: PDB Entry ID
  • entity_id: the entity identifier of a PDB Entity; for what is PDB Entity? please look at this link
  • chain_id: the chain identifier of a PDB Chain
  • struct_asym_id: the chain identifier of a PDB Chain (unique across all PDB Entity)
  • Entry: UniProt Entry ID
  • UniProt: UniProt Isoform ID
  • is_canonical: whether the UniProt Isoform is the canonical sequence of that UniProt Entry
  • identity: sequence identity between the corresponding PDB Chain's Sequence(complete SEQRES) and UniProt Isoform's Sequence
  • unp_range: mapped range of the UniProt Isoform's Sequence with its corresponding PDB Chain's Sequence (Index from 1)
  • pdb_range: mapped range of the PDB Chain's Sequence Sequence with its corresponding UniProt Isoform's (Index from 1)
  • new_unp_range: fixed(deal with InDel) mapped range of the UniProt Isoform's Sequence with its corresponding PDB Chain's Sequence (Index from 1)
  • new_pdb_range: fixed(deal with InDel) mapped range of the PDB Chain's Sequence Sequence with its corresponding UniProt Isoform's (Index from 1)
  • conflict_pdb_range: the chain's residue index of residue confilct with UniProt isoform sequence in the mapped range(Index from 1)
  • select_tag: whether in the recommanded representative set
  • select_rank: the rank among all the chains (1st denoted as the best)
In [5]:
%time df1 = demo.pipe_select_mo().result()
# NOTE: df1里的所有结果是该UniProt匹配上的所有PDB链
df1
# NOTE: 程序推荐的是select_tag为True的,根据一系列打分排名; 同时考虑了覆盖范围,尽多选择覆盖完该UniProt Isoform序列的结构
Wall time: 1.07 s
Out[5]:
UniProt chain_id entity_id identity is_canonical pdb_id struct_asym_id pdb_range unp_range Entry ... resolution experimental_method_class experimental_method multi_method revision_date deposition_date 1/resolution id_score select_tag select_rank
0 P21359 A 1 0.94 True 1nf1 A [[1,333]] [[1198,1551]] P21359 ... 2.500 x-ray X-ray diffraction False 20171004 19980708 0.400000 -65 False 16
1 P21359 A 1 1.00 True 3pg7 A [[1,256]] [[1581,1837]] P21359 ... 2.189 x-ray X-ray diffraction False 20110713 20101031 0.456830 -65 False 5
2 P21359 B 1 1.00 True 3pg7 B [[1,256]] [[1581,1837]] P21359 ... 2.189 x-ray X-ray diffraction False 20110713 20101031 0.456830 -66 False 6
3 P21359 B 2 0.94 True 6v65 B [[2,329]] [[1203,1551]] P21359 ... 2.763 x-ray X-ray diffraction False 20200805 20191204 0.361925 -66 False 11
4 P21359 A 1 1.00 True 2d4q A [[1,257]] [[1581,1837]] P21359 ... 2.300 x-ray X-ray diffraction False 20110713 20051022 0.434783 -65 False 2
5 P21359 B 1 1.00 True 2d4q B [[1,257]] [[1581,1837]] P21359 ... 2.300 x-ray X-ray diffraction False 20110713 20051022 0.434783 -66 False 4
6 P21359 A 1 0.94 True 3peg A [[5,172],[174,290]] [[1566,1733],[1721,1837]] P21359 ... 2.524 x-ray X-ray diffraction False 20190717 20101026 0.396197 -65 False 9
7 P21359 B 2 0.92 True 6ob3 B [[2,256]] [[1209,1484]] P21359 ... 2.100 x-ray X-ray diffraction False 20191113 20190319 0.476190 -66 False 14
8 P21359 D 2 0.92 True 6ob3 D [[2,256]] [[1209,1484]] P21359 ... 2.100 x-ray X-ray diffraction False 20191113 20190319 0.476190 -68 False 13
9 P21359 B 2 0.92 True 6ob2 B [[2,256]] [[1209,1484]] P21359 ... 2.845 x-ray X-ray diffraction False 20191113 20190319 0.351494 -66 False 15
10 P21359 D 2 0.92 True 6ob2 D [[2,256]] [[1209,1484]] P21359 ... 2.845 x-ray X-ray diffraction False 20191113 20190319 0.351494 -68 False 12
11 P21359 A 1 0.98 True 3p7z A [[5,276]] [[1566,1837]] P21359 ... 2.650 x-ray X-ray diffraction False 20190717 20101013 0.377358 -65 False 3
12 P21359 B 1 0.98 True 3p7z B [[5,276]] [[1566,1837]] P21359 ... 2.650 x-ray X-ray diffraction False 20190717 20101013 0.377358 -66 True 1
13 P21359 B 2 0.94 True 6v6f B [[2,329]] [[1203,1551]] P21359 ... 2.542 x-ray X-ray diffraction False 20200805 20191205 0.393391 -66 True 10
14 P21359 A 1 0.99 True 2e2x A [[6,277]] [[1566,1837]] P21359 ... 2.500 x-ray X-ray diffraction False 20110713 20061118 0.400000 -65 False 7
15 P21359 B 1 0.99 True 2e2x B [[6,277]] [[1566,1837]] P21359 ... 2.500 x-ray X-ray diffraction False 20110713 20061118 0.400000 -66 False 8

16 rows × 48 columns

Prepare Interactome3D MetaData

下面这里的代码只需要运行一次,以后再也不用运行,包括重启、重新打开代码文件时也是不用再运行;

from pdb_profiling.processors.i3d.api import Interactome3D

Interactome3D.pipe_init_interaction_meta().result()
In [6]:
# NOTE: 如果未运行过如下代码,可以把#号注释去掉
# Only need to run once
# from pdb_profiling.processors.i3d.api import Interactome3D

# Interactome3D.pipe_init_interaction_meta().result()

Homomeric Protein

Interaction metadata comes from Interactome3D

  • _1: denoted as the partner chain 1
  • _2: denoted as the partner chain 2
  • assembly_id
    • 0 stands for asymmetric unit
    • 1 stands for biological assembly 1
    • 2 stands for biological assembly 2
    • and so on
    • for what is asymmetric unit & biological assembly? please click the link
  • model_id: the model ID of the chain in the corresponding biological assembly PDB format file
    • 0 denoted as the first model
  • unp_range_DSC: the Dice Similarity Coefficient of new_unp_range_1 & new_unp_range_2
  • interface_range_1: the range of the interaction's interface in the aspect of partner1 chain (Index from 1)
  • interface_range_2: the range of the interaction's interface in the aspect of partner2 chain (Index from 1)
  • unp_interface_range_1: the range of the interaction's interface in the aspect of partner1 chain (mapped to the UniProt Isoforom)
  • unp_interface_range_2: the range of the interaction's interface in the aspect of partner2 chain (mapped to the UniProt Isoforom)
  • i_select_tag: whether in the recommanded interaction representative set
  • i_select_rank: the rank among all the interacting-chains (1st denoted as the best)
In [7]:
%time df2 = demo.pipe_select_ho(run_as_completed=True, progress_bar=tqdm).result()
# NOTE: df2里的所有结果是该UniProt匹配上的所有同聚体相互作用链;每一行就是一对相互作用 (同属于一个蛋白的两条链相互作用);
df2
# NOTE: 程序推荐的是i_select_tag为True的,根据一系列打分排名; 同时考虑了interface覆盖范围,尽多选择各种类型同聚体相互作用结构
100%|██████████| 10/10 [00:02<00:00,  3.38it/s]
Wall time: 4.25 s
Out[7]:
entity_id_1 chain_id_1 struct_asym_id_1 struct_asym_id_in_assembly_1 asym_id_rank_1 model_id_1 molecule_type_1 surface_range_1 interface_range_1 entity_id_2 ... id_score_2 select_tag_2 select_rank_2 in_i3d best_select_rank unp_range_DSC unp_interface_range_1 unp_interface_range_2 i_select_tag i_select_rank
0 1 A A A 1 1 polypeptide(L) [[7,44],[46,47],[49,62],[64,82],[84,84],[86,25... [[50,51],[53,53],[86,86],[91,91],[167,168],[17... 1 ... -66 True 1 False 1 1.0 ((1611, 1612), (1614, 1614), (1647, 1647), (16... ((1611, 1612), (1614, 1614), (1647, 1647), (16... False 9
1 1 A A A 1 1 polypeptide(L) [[7,44],[46,47],[49,62],[64,82],[84,84],[86,25... [[50,51],[53,53],[86,86],[91,91],[167,168],[17... 1 ... -66 True 1 True 1 1.0 ((1611, 1612), (1614, 1614), (1647, 1647), (16... ((1611, 1612), (1614, 1614), (1647, 1647), (16... False 10
2 1 A A A 1 1 polypeptide(L) [[28,44],[47,48],[50,52],[54,62],[64,81],[83,8... [[51,52],[54,54],[87,87],[92,92],[168,169],[17... 1 ... -66 False 8 False 7 1.0 ((1611, 1612), (1614, 1614), (1647, 1647), (16... ((1611, 1612), (1614, 1614), (1647, 1647), (16... True 4
3 1 A A A 1 1 polypeptide(L) [[28,44],[47,48],[50,52],[54,62],[64,81],[83,8... [[51,52],[54,54],[87,87],[92,92],[168,169],[17... 1 ... -66 False 8 True 7 1.0 ((1611, 1612), (1614, 1614), (1647, 1647), (16... ((1611, 1612), (1614, 1614), (1647, 1647), (16... False 5
4 1 A A A 1 1 polypeptide(L) [[1,11],[13,25],[27,28],[30,42],[44,236],[238,... [[31,32],[34,34],[67,67],[72,72],[148,149],[15... 1 ... -66 False 4 False 2 1.0 ((1611, 1612), (1614, 1614), (1647, 1647), (16... ((1590, 1590), (1611, 1612), (1614, 1614), (16... False 7
5 1 A A A 1 1 polypeptide(L) [[1,11],[13,25],[27,28],[30,42],[44,236],[238,... [[31,32],[34,34],[67,67],[72,72],[148,149],[15... 1 ... -66 False 4 True 2 1.0 ((1611, 1612), (1614, 1614), (1647, 1647), (16... ((1590, 1590), (1611, 1612), (1614, 1614), (16... False 8
6 1 A A A 1 1 polypeptide(L) [[1,24],[28,235],[237,238],[240,256]] [[31,32],[34,34],[67,67],[72,72],[148,149],[15... 1 ... -66 False 6 False 5 1.0 ((1611, 1612), (1614, 1614), (1647, 1647), (16... ((1611, 1612), (1614, 1614), (1647, 1647), (16... False 6
7 2 B B B 1 1 polypeptide(L) [[12,48],[50,53],[55,73],[75,76],[78,80],[82,8... [[228,228],[231,232],[234,235],[237,238],[241,... 2 ... -68 False 13 False 13 1.0 ((1456, 1456), (1459, 1460), (1462, 1463), (14... ((1298, 1298), (1302, 1302), (1306, 1306), (14... True 1
8 2 B B B 1 1 polypeptide(L) [[12,48],[50,53],[55,76],[78,80],[82,85],[87,1... [[125,125],[231,231],[234,235],[237,238],[241,... 2 ... -68 False 12 False 12 1.0 ((1332, 1332), (1459, 1459), (1462, 1463), (14... ((1306, 1306), (1422, 1422), (1425, 1425), (14... True 2
9 1 A A A 1 1 polypeptide(L) [[24,30],[32,44],[46,61],[63,153],[177,269],[2... [[95,96],[99,100],[102,103],[107,107],[110,111... 1 ... -65 False 9 True 9 1.0 ((1656, 1657), (1660, 1661), (1663, 1664), (16... ((1656, 1657), (1660, 1661), (1663, 1664), (16... True 3

10 rows × 115 columns

Heteromeric Protein

Interaction metadata comes from Interactome3D

  • i_group: the Heteromeric Interaction Group
In [8]:
# NOTE: 给出目标蛋白的相互作用蛋白
%time df3 = demo.pipe_select_he(run_as_completed=True, progress_bar=tqdm).result()
# NOTE: df3里的所有结果是该UniProt匹配上的所有异聚体相互作用链;每一行就是一对相互作用 (属于两个不同个蛋白的两条链相互作用);
df3
# NOTE: 程序推荐的是i_select_tag为True的,根据一系列打分排名; 同时考虑了interface覆盖范围,尽多选择同一对异聚体相互作用下的各种相互作用结构
# NOTE: 输入的UniProt Isoform可能是UniProt_1也可能是UniProt_2
# NOTE: 同一对异聚体相互作用可用i_group认定
100%|██████████| 4/4 [00:01<00:00,  2.17it/s]
Wall time: 6.39 s
Out[8]:
entity_id_1 chain_id_1 struct_asym_id_1 struct_asym_id_in_assembly_1 asym_id_rank_1 model_id_1 molecule_type_1 surface_range_1 interface_range_1 entity_id_2 ... id_score_2 select_tag_2 select_rank_2 in_i3d best_select_rank unp_interface_range_1 unp_interface_range_2 i_select_tag i_select_rank i_group
0 2 B B B 1 1 polypeptide(L) [[4,59],[61,83],[85,86],[88,91],[93,137],[139,... [[32,33],[35,35],[71,72],[75,77],[81,82],[85,8... 3 ... -67 False 2 False -1 ((328, 329), (331, 331), (367, 368), (371, 373... ((12, 12), (17, 17), (21, 21), (25, 25), (29, ... False -1 (P01116-2, P21359-3)
1 2 B B B 1 1 polypeptide(L) [[4,59],[61,83],[85,86],[88,91],[93,137],[139,... [[32,33],[35,35],[71,72],[75,77],[81,82],[85,8... 3 ... -67 False 2 False -1 ((328, 329), (331, 331), (367, 368), (371, 373... ((12, 12), (17, 17), (21, 21), (25, 25), (29, ... False -1 (P01116, P21359-3)
2 2 B B B 1 1 polypeptide(L) [[4,59],[61,83],[85,86],[88,91],[93,137],[139,... [[32,33],[35,35],[71,72],[75,77],[81,82],[85,8... 3 ... -67 False 2 False 2 ((1233, 1234), (1236, 1236), (1272, 1273), (12... ((12, 12), (17, 17), (21, 21), (25, 25), (29, ... False 13 (P01116-2, P21359-2)
3 2 B B B 1 1 polypeptide(L) [[4,59],[61,83],[85,86],[88,91],[93,137],[139,... [[32,33],[35,35],[71,72],[75,77],[81,82],[85,8... 3 ... -67 False 2 False 2 ((1233, 1234), (1236, 1236), (1272, 1273), (12... ((12, 12), (17, 17), (21, 21), (25, 25), (29, ... False 13 (P01116, P21359-2)
4 2 B B B 1 1 polypeptide(L) [[4,59],[61,83],[85,86],[88,91],[93,137],[139,... [[32,33],[35,35],[71,72],[75,77],[81,82],[85,8... 3 ... -67 False 2 False 2 ((1233, 1234), (1236, 1236), (1272, 1273), (12... ((12, 12), (17, 17), (21, 21), (25, 25), (29, ... False 13 (P01116-2, P21359-6)
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
187 1 C C C 1 1 polypeptide(L) [[2,20],[22,23],[25,51],[53,53],[55,55],[57,72... [[12,14],[18,18],[22,22],[26,26],[28,28],[30,3... 2 ... -68 False 10 True 5 ((11, 13), (17, 17), (21, 21), (25, 25), (27, ... ((1233, 1234), (1236, 1237), (1272, 1278), (12... False 8 (P01116, P21359-2)
188 1 C C C 1 1 polypeptide(L) [[2,20],[22,23],[25,51],[53,53],[55,55],[57,72... [[12,14],[18,18],[22,22],[26,26],[28,28],[30,3... 2 ... -68 False -1 True -1 ((11, 13), (17, 17), (21, 21), (25, 25), (27, ... ((328, 329), (331, 332), (367, 373), (377, 378... False -1 (P01116, P21359-5)
189 1 C C C 1 1 polypeptide(L) [[2,20],[22,23],[25,51],[53,53],[55,55],[57,72... [[12,14],[18,18],[22,22],[26,26],[28,28],[30,3... 2 ... -68 False 4 True 4 ((11, 13), (17, 17), (21, 21), (25, 25), (27, ... ((1233, 1234), (1236, 1237), (1272, 1278), (12... False 8 (P01116, P21359-4)
190 1 C C C 1 1 polypeptide(L) [[2,20],[22,23],[25,51],[53,53],[55,55],[57,72... [[12,14],[18,18],[22,22],[26,26],[28,28],[30,3... 2 ... -68 False 13 True 5 ((11, 13), (17, 17), (21, 21), (25, 25), (27, ... ((1233, 1234), (1236, 1237), (1272, 1278), (12... False 8 (P01116, P21359)
191 1 C C C 1 1 polypeptide(L) [[2,20],[22,23],[25,51],[53,53],[55,55],[57,72... [[12,14],[18,18],[22,22],[26,26],[28,28],[30,3... 2 ... -68 False 10 True 5 ((11, 13), (17, 17), (21, 21), (25, 25), (27, ... ((1233, 1234), (1236, 1237), (1272, 1278), (12... False 8 (P01116, P21359-6)

192 rows × 119 columns

summary: pipe_select_mo是给出目标蛋白的单体信息;pipe_select_ho、pipe_select_he分别给出目标蛋白的同聚体相互作用和异聚体相互作用蛋白相关信息;和mo给出的列信息多数一样但是有两个蛋白

Mapping Between Sites in UniProt Isoform and PDB Chain

In [9]:
df1[df1.select_tag.eq(True)]
Out[9]:
UniProt chain_id entity_id identity is_canonical pdb_id struct_asym_id pdb_range unp_range Entry ... resolution experimental_method_class experimental_method multi_method revision_date deposition_date 1/resolution id_score select_tag select_rank
12 P21359 B 1 0.98 True 3p7z B [[5,276]] [[1566,1837]] P21359 ... 2.650 x-ray X-ray diffraction False 20190717 20101013 0.377358 -66 True 1
13 P21359 B 2 0.94 True 6v6f B [[2,329]] [[1203,1551]] P21359 ... 2.542 x-ray X-ray diffraction False 20200805 20191205 0.393391 -66 True 10

2 rows × 48 columns

In [10]:
# NOTE: 选定一个UniProt Isoform与PDB chain的对应关系
# NOTE: 在df1的select_tag为true的PDB链里选择覆盖了你的突变的结构; 有没有覆盖你可以看new_unp_range这个区间有没有覆盖你的突变位置
record = df1.loc[12]
In [11]:
# show it
record
Out[11]:
UniProt                                                                 P21359
chain_id                                                                     B
entity_id                                                                    1
identity                                                                  0.98
is_canonical                                                              True
pdb_id                                                                    3p7z
struct_asym_id                                                               B
pdb_range                                                            [[5,276]]
unp_range                                                        [[1566,1837]]
Entry                                                                   P21359
range_diff                                                                 [0]
sifts_range_tag                                                           Safe
repeated                                                                 False
reversed                                                                 False
InDel_sum                                                                    0
new_pdb_range                                                        [[5,276]]
new_unp_range                                                    [[1566,1837]]
conflict_pdb_range                                                 ((44, 44),)
unp_len                                                                   2839
BINDING_LIGAND_COUNT                                                        16
BINDING_LIGAND_INDEX         [[80, 80], [92, 95], [101, 102], [110, 110], [...
OBS_COUNT                                                                  270
OBS_INDEX                                                           [[7, 276]]
OBS_RATIO_SUM                                                           269.18
ARTIFACT_INDEX                                                        [[1, 4]]
NON_COUNT                                                                    0
NON_INDEX                                                                   []
SEQRES_COUNT                                                               276
STD_COUNT                                                                  276
STD_INDEX                                                           [[1, 276]]
UNK_COUNT                                                                    0
UNK_INDEX                                                                   []
ca_p_only                                                                False
molecule_type                                                   polypeptide(L)
OBS_STD_INDEX                                                      ((7, 276),)
OBS_STD_COUNT                                                              270
RAW_BS                                                               0.0882066
RAW_BS_IG3                                                           0.0938424
resolution                                                                2.65
experimental_method_class                                                x-ray
experimental_method                                          X-ray diffraction
multi_method                                                             False
revision_date                                                         20190717
deposition_date                                                       20101013
1/resolution                                                          0.377358
id_score                                                                   -66
select_tag                                                                True
select_rank                                                                  1
Name: 12, dtype: object
In [12]:
# NOTE: 简单查看结构静态图
DisplayPDB(True).show(record['pdb_id'])
Asymmetric unit of 3p7z Biological assembly 1 of 3p7z
  • unp_residue_number: residue index in the aspect of the UniProt Isoform's Sequence (Index from 1)
  • residue_number: residue index in the aspect of the PDB Chain's Sequence (SEQRES, Index from 1)
  • author_residue_number: residue index in the aspect of the PDB Chain's Sequence but assigned by the author of this PDB Entry

summary: unp_residue_number就是unp对应序列的从1开始计数的索引位置; resiude_number是对pdb链从1开始计数的索引; author_residue_numer是pdb文件作者定义的索引

因为unp_residue_number和author_residue_numer可能会不一致,而多数软件需要author_residue_number作为输入,所以要将位点统一转为author_residue_nume再进行使用; (i.e. unp上的12号位在pdb链上不一定是12号)

一般没法事先知道pdb与unp的标号是否一致,这是一个索引映射的问题;比如unp是100长度,索引就是1,2,..100 而与这个unp匹配上的PDB晶体结构,它的对应匹配上的链是长度为91;作者给这条链的标号是66,67,...156

In [13]:
PDB(record['pdb_id']).get_expanded_map_res_df(
    record['UniProt'], 
    record['new_unp_range'], 
    record['new_pdb_range'], 
    struct_asym_id=record['struct_asym_id']).result()
Out[13]:
unp_residue_number residue_number UniProt author_insertion_code author_residue_number chain_id entity_id multiple_conformers observed_ratio pdb_id residue_name struct_asym_id
0 1566 5 P21359 1545 B 1 NaN 0.0 3p7z SER B
1 1567 6 P21359 1546 B 1 NaN 0.0 3p7z SER B
2 1568 7 P21359 1547 B 1 NaN 1.0 3p7z LYS B
3 1569 8 P21359 1548 B 1 NaN 1.0 3p7z PHE B
4 1570 9 P21359 1549 B 1 NaN 1.0 3p7z GLU B
... ... ... ... ... ... ... ... ... ... ... ... ...
267 1833 272 P21359 1812 B 1 NaN 1.0 3p7z LEU B
268 1834 273 P21359 1813 B 1 NaN 1.0 3p7z SER B
269 1835 274 P21359 1814 B 1 NaN 1.0 3p7z GLN B
270 1836 275 P21359 1815 B 1 NaN 1.0 3p7z PRO B
271 1837 276 P21359 1816 B 1 NaN 1.0 3p7z ASP B

272 rows × 12 columns

Example: 原突变(p.P1836R) $\rightarrow$ 于3p7z的B链中变为(P1815R) $\rightarrow$ 作为foldx的突变位置输入变为(PB1815R)

在这里关注的是1836$\rightarrow$1815的转变

当然同时可以通过residue_name列或df1的conflict_pdb_range列确认142位是不是氨基酸PRO

WARNING: 如果你的位点的author_insertion_code非空或者author_residue_number小于等于0, 请联系学委, 须进行额外步骤

Batch Retrieve

下面展示如果有多个UniProt Isoform的批量处理方法

In [14]:
# optional
res = SIFTSs(('Q00987-2', 'Q00987-10', 'O15350')).fetch('pipe_select_mo').run(tqdm).result()
# NOTE: 传入tqdm与否不影响运行
# NOTE: res is a list and the order of the result can be different from the original input order
100%|██████████| 3/3 [00:06<00:00,  2.24s/it]
In [15]:
res[0]
Out[15]:
UniProt chain_id entity_id identity is_canonical pdb_id struct_asym_id pdb_range unp_range Entry ... resolution experimental_method_class experimental_method multi_method revision_date deposition_date 1/resolution id_score select_tag select_rank
0 O15350 A 1 0.99 True 3vd2 A [[13,210]] [[115,312]] O15350 ... 4.000000 x-ray X-ray diffraction False 20120725 20120104 0.250000 -65 False 28
1 O15350 B 1 0.99 True 3vd2 B [[13,210]] [[115,312]] O15350 ... 4.000000 x-ray X-ray diffraction False 20120725 20120104 0.250000 -66 False 36
2 O15350 C 1 0.99 True 3vd2 C [[13,210]] [[115,312]] O15350 ... 4.000000 x-ray X-ray diffraction False 20120725 20120104 0.250000 -67 False 29
3 O15350 D 1 0.99 True 3vd2 D [[13,210]] [[115,312]] O15350 ... 4.000000 x-ray X-ray diffraction False 20120725 20120104 0.250000 -68 False 41
4 O15350 I 1 0.99 True 3vd2 E [[13,210]] [[115,312]] O15350 ... 4.000000 x-ray X-ray diffraction False 20120725 20120104 0.250000 -73 False 30
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
109 O15350 F 1 0.92 True 5hob F [[3,50]] [[351,398]] O15350 ... 1.220013 x-ray X-ray diffraction False 20161019 20160119 0.819663 -70 False 64
110 O15350 G 1 0.92 True 5hob G [[3,50]] [[351,398]] O15350 ... 1.220013 x-ray X-ray diffraction False 20161019 20160119 0.819663 -71 False 53
111 O15350 H 1 0.92 True 5hob H [[3,50]] [[351,398]] O15350 ... 1.220013 x-ray X-ray diffraction False 20161019 20160119 0.819663 -72 False 59
112 O15350 A 1 0.92 True 5hoc A [[3,50]] [[351,398]] O15350 ... 1.360078 x-ray X-ray diffraction False 20161130 20160119 0.735252 -65 False 60
113 O15350 B 1 0.92 True 5hoc B [[3,50]] [[351,398]] O15350 ... 1.360078 x-ray X-ray diffraction False 20161130 20160119 0.735252 -66 False 61

114 rows × 48 columns

In [16]:
res[1]
Out[16]:
UniProt chain_id entity_id identity is_canonical pdb_id struct_asym_id pdb_range unp_range Entry ... resolution experimental_method_class experimental_method multi_method revision_date deposition_date 1/resolution id_score select_tag select_rank
0 Q00987-2 A 1 1.00 False 4jv9 A [[1,10]] [[18,27]] Q00987 ... 2.500 x-ray X-ray diffraction False 20130605 20130325 0.400000 -65 False -1
1 Q00987-2 C 3 0.97 False 5mnj C [[23,86]] [[233,296]] Q00987 ... 2.160 x-ray X-ray diffraction False 20191016 20161213 0.462963 -67 False 12
2 Q00987-2 G 3 0.97 False 5mnj G [[23,86]] [[233,296]] Q00987 ... 2.160 x-ray X-ray diffraction False 20191016 20161213 0.462963 -71 False 11
3 Q00987-2 A 1 1.00 False 4ogv A [[1,11]] [[17,27]] Q00987 ... 2.197 x-ray X-ray diffraction False 20140618 20140116 0.455166 -65 False -1
4 Q00987-2 B 1 1.00 False 4ogv B [[1,11]] [[17,27]] Q00987 ... 2.197 x-ray X-ray diffraction False 20140618 20140116 0.455166 -66 False -1
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
208 Q00987-2 A 1 1.00 False 6q9o A [[2,12]] [[17,27]] Q00987 ... 1.210 x-ray X-ray diffraction False 20190724 20181218 0.826446 -65 False -1
209 Q00987-2 B 1 1.00 False 6q9o B [[2,12]] [[17,27]] Q00987 ... 1.210 x-ray X-ray diffraction False 20190724 20181218 0.826446 -66 False -1
210 Q00987-2 A 1 1.00 False 6q9h A [[2,12]] [[17,27]] Q00987 ... 2.000 x-ray X-ray diffraction False 20190724 20181218 0.500000 -65 False -1
211 Q00987-2 D 2 1.00 False 3mqs B [[1,10]] [[199,208]] Q00987 ... 2.400 x-ray X-ray diffraction False 20110713 20100428 0.416667 -68 False 14
212 Q00987-2 B 2 1.00 False 5wts B [[3,24]] [[6,27]] Q00987 ... 3.004 x-ray X-ray diffraction False 20191106 20161214 0.332889 -66 False -1

213 rows × 48 columns

In [ ]: