3SBW | pdb_00003sbw

Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1

• PDB DOI: https://doi.org/10.2210/pdb3SBW/pdb

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


• Deposited: 2011-06-06 Released: 2011-07-13 
• Deposition Author(s): Lazar-Molnar, E., Ramagopal, U.A., Cao, E., Nathenson, S.G., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and human PD-L1

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.89 kDa 
• Atom Count: 3,573 
• Modeled Residue Count: 432 
• Deposited Residue Count: 456 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A, B	117	Mus musculus	Mutation(s): 2  Gene Names: Pdcd1, Pd1
UniProt
Find proteins for Q02242 (Mus musculus) Explore Q02242  Go to UniProtKB:  Q02242

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death 1 ligand 1	C	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.778	α = 90
b = 62.843	β = 90
c = 160.863	γ = 90

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: 2011-07-13 
Deposition Author(s): Lazar-Molnar, E., Ramagopal, U.A., Cao, E., Nathenson, S.G., Almo, S.C.

Revision History  

• Version 1.0: 2011-07-13
  Type: Initial release
  
• Version 1.1: 2013-09-18
  Changes: Derived calculations
• Version 1.2: 2016-08-03
  Changes: Derived calculations
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary