5GRJ | pdb_00005grj

Crystal structure of human PD-L1 with monoclonal antibody avelumab

PDB DOI: https://doi.org/10.2210/pdb5GRJ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-08-11 Released: 2016-11-02
Deposition Author(s): Liu, K., Tan, S., Chai, Y., Chen, D., Song, H., Zhang, C.W.-H., Shi, Y., Liu, J., Tan, W., Lyu, J., Gao, S., Yan, J., Qi, J., Gao, G.F.
Funding Organization(s): the Ministry of Science and Technology of China, Grand S&T project of China Health and Family Planning Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free:
0.238 (Depositor), 0.241 (DCC)
R-Value Work:
0.203 (Depositor), 0.204 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structural basis of anti-PD-L1 monoclonal antibody avelumab for tumor therapy.

Liu, K., Tan, S., Chai, Y., Chen, D., Song, H., Zhang, C.W., Shi, Y., Liu, J., Tan, W., Lyu, J., Gao, S., Yan, J., Qi, J., Gao, G.F.

(2017) Cell Res 27: 151-153

PubMed: 27573173 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/cr.2016.102
Primary Citation Related Structures:
5GRJ

Organizational Affiliation

College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.

Macromolecule Content

Total Structure Weight: 49.83 kDa
Atom Count: 3,398
Modeled Residue Count: 439
Deposited Residue Count: 451
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
avelumab H chain	A [auth H]	120	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
avelumab L chain	B [auth L]	110	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	C [auth A]	221	Homo sapiens	Mutation(s): 0 Gene Names: PDL1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZQ7 (Homo sapiens) Explore Q9NZQ7 Go to UniProtKB: Q9NZQ7
PHAROS: Q9NZQ7 GTEx: ENSG00000120217
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NZQ7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.21 Å
R-Value Free: 0.238 (Depositor), 0.241 (DCC)
R-Value Work: 0.203 (Depositor), 0.204 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.87	α = 90
b = 98.151	β = 108.43
c = 62.036	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Funding Organization	Location	Grant Number
the Ministry of Science and Technology of China	China	2013CB531502, 2014CB542503
Grand S&T project of China Health and Family Planning Commission	China	013ZX10004608-002, 2016ZX10004201-009

Revision History (Full details and data files)

Version 1.0: 2016-11-02
Type: Initial release
Version 1.1: 2017-01-18
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary