3RRQ | pdb_00003rrq

Crystal structure of the extracellular domain of human PD-1

• PDB DOI: https://doi.org/10.2210/pdb3RRQ/pdb

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


• Deposited: 2011-04-29 Released: 2012-05-16 
• Deposition Author(s): Lazar-Molnar, E., Ramagopal, U.A., Nathenson, S.G., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.249 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the extracellular domain of human PD-1

Lazar-Molnar, E., Ramagopal, U.A., Nathenson, S.G., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.45 kDa 
• Atom Count: 903 
• Modeled Residue Count: 108 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A	129	Homo sapiens	Mutation(s): 1  Gene Names: PD-1, PD1, PDCD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15116 (Homo sapiens) Explore Q15116  Go to UniProtKB:  Q15116
PHAROS:  Q15116 GTEx:  ENSG00000188389

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.249 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.02	α = 90
b = 46.02	β = 90
c = 187.395	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-16 
Deposition Author(s): Lazar-Molnar, E., Ramagopal, U.A., Nathenson, S.G., Almo, S.C.

Revision History  

• Version 1.0: 2012-05-16
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary