Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26385.79 
• Atom Count: 1651 
• Residue Count: 233 
• Unique protein chains: 2

4ZQK

Structure of the complex of human programmed death-1 (PD-1) and its ligand PD-L1.

• DOI: 10.2210/pdb4ZQK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


• Deposited: 2015-05-10 Released: 2015-11-04 
• Deposition Author(s): Zak, K.M., Dubin, G., Holak, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.253 
• R-Value Work: 0.207 

Literature

Structure of the Complex of Human Programmed Death 1, PD-1, and Its Ligand PD-L1.

Zak, K.M., Kitel, R., Przetocka, S., Golik, P., Guzik, K., Musielak, B., Domling, A., Dubin, G., Holak, T.A.

(2015) Structure 23: 2341-2348

• PubMed: 26602187 
• DOI: 10.1016/j.str.2015.09.010
• Primary Citation of Related Structures:  
  5C3T


• PubMed Abstract: 
  

Targeting the PD-1/PD-L1 immunologic checkpoint with monoclonal antibodies has recently provided breakthrough progress in the treatment of melanoma, non-small cell lung cancer, and other types of cancer. Small-molecule drugs interfering with this pathway are highly awaited, but their development is hindered by insufficient structural information. This study reveals the molecular details of the human PD-1/PD-L1 interaction based on an X-ray structure of the complex. First, it is shown that the ligand binding to human PD-1 is associated with significant plasticity within the receptor. Second, a detailed molecular map of the interaction surface is provided, allowing definition of the regions within both interacting partners that may likely be targeted by small molecules.

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Organizational Affiliation: 

Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland; Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Programmed cell death 1 ligand 1	A	115	Homo sapiens	Mutation(s): 0  Gene Names: CD274 (B7H1, PDCD1L1, PDCD1LG1, PDL1)
Find proteins for Q9NZQ7 (Homo sapiens) Go to Gene View: CD274 Go to UniProtKB:  Q9NZQ7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Programmed cell death protein 1	B	118	Homo sapiens	Mutation(s): 1  Gene Names: PDCD1 (PD1)
Find proteins for Q15116 (Homo sapiens) Go to Gene View: PDCD1 Go to UniProtKB:  Q15116

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.253 
• R-Value Work: 0.207 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 70.862	α = 90.00
b = 70.862	β = 90.00
c = 114.367	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-05-10 
• Released Date: 2015-11-04 
• Deposition Author(s): Zak, K.M., Dubin, G., Holak, T.A.

Revision History 

• Version 1.0: 2015-11-04
  Type: Initial release
• Version 1.1: 2015-12-09
  Type: Database references
• Version 1.2: 2015-12-16
  Type: Database references