6YCR | pdb_00006ycr

Structure of human PD-L1 in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb6YCR/pdb

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

Deposited: 2020-03-18 Released: 2021-02-03
Deposition Author(s): Magiera-Mularz, K., Grudnik, P., Kuska, K., Holak, T.A., Dubin, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free:
0.180 (Depositor), 0.184 (DCC)
R-Value Work:
0.148 (Depositor), 0.167 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6YCR

This is version 1.1 of the entry. See complete history.

Literature

Macrocyclic Peptide Inhibitor of PD-1/PD-L1 Immune Checkpoint

Magiera-Mularz, K., Kuska, K., Skalniak, L., Grudnik, P., Musielak, B., Plewka, J., Kocik, J., Stec, M., Weglarczyk, K., Sala, D., Wladyka, B., Siedlar, M., Holak, T.A., Dubin, G.

(2020) Adv Ther

DOI: https://doi.org/10.1002/adtp.202000195

Macromolecule Content

Total Structure Weight: 16.37 kDa
Atom Count: 1,471
Modeled Residue Count: 133
Deposited Residue Count: 142
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	A	128	Homo sapiens	Mutation(s): 0 Gene Names: CD274, B7H1, PDCD1L1, PDCD1LG1, 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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FFIVIRDRVFR(CCS)G(NH2)	B	14	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CCS Query on CCS	B	L-PEPTIDE LINKING	C₅ H₉ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.180 (Depositor), 0.184 (DCC)
R-Value Work: 0.148 (Depositor), 0.167 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.708	α = 90
b = 86.708	β = 90
c = 86.708	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-02-03

Deposition Author(s):

Magiera-Mularz, K.

Revision History (Full details and data files)

Version 1.0: 2021-02-03
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.