3BP6 | pdb_00003bp6

Crystal structure of the mouse PD-1 Mutant and PD-L2 complex

• PDB DOI: https://doi.org/10.2210/pdb3BP6/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-12-18 Released: 2009-02-24 
• Deposition Author(s): Yan, Q., Lazar-Molnar, E., Cao, E., Ramagopal, U.A., Toro, R., Nathenson, S.G., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the mouse PD-1 A99L and PD-L2 complex

Yan, Q., Lazar-Molnar, E., Cao, E., Ramagopal, U.A., Toro, R., 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)

Macromolecule Content 

• Total Structure Weight: 36.38 kDa 
• Atom Count: 2,761 
• Modeled Residue Count: 298 
• Deposited Residue Count: 319 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A	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 2	B	202	Mus musculus	Mutation(s): 0  Gene Names: Pdcd1lg2, B7dc, Btdc, Cd273, Pdl2
UniProt
Find proteins for Q9WUL5 (Mus musculus) Explore Q9WUL5  Go to UniProtKB:  Q9WUL5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B], E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.747	α = 90
b = 84.335	β = 108
c = 52.281	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-24 
Deposition Author(s): Yan, Q., Lazar-Molnar, E., Cao, E., Ramagopal, U.A., Toro, R., Nathenson, S.G., Almo, S.C.

Revision History  

• Version 1.0: 2009-02-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.5: 2023-12-27
  Changes: Derived calculations
• Version 1.6: 2024-11-06
  Changes: Structure summary