4Z18 | pdb_00004z18

CRYSTAL STRUCTURE OF HUMAN PD-L1

• PDB DOI: https://doi.org/10.2210/pdb4Z18/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2015-03-27 Released: 2015-04-15 
• Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Samantha, D., Hillerich, B., Seidel, R.D., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.246 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

CRYSTAL STRUCTURE OF HUMAN PD-L1

Fedorov, A.A., Fedorov, E.V., Samantha, D., Hillerich, B., Seidel, R.D., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.95 kDa 
• Atom Count: 3,484 
• Modeled Residue Count: 422 
• Deposited Residue Count: 444 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	A, B	222	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.246 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.03	α = 90
b = 91.48	β = 90
c = 135.735	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CBASS	data collection
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-15 
Deposition Author(s): Fedorov, A.A., Fedorov, E.V., Samantha, D., Hillerich, B., Seidel, R.D., Almo, S.C.

Revision History  

• Version 1.0: 2015-04-15
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary