5JXE

Human PD-1 ectodomain complexed with Pembrolizumab Fab

• PDB DOI: https://doi.org/10.2210/pdb5JXE/pdb

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


• Deposited: 2016-05-13 Released: 2016-08-10 
• Deposition Author(s): Na, Z., Bharath, S.R., Song, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.261 
• R-Value Observed: 0.262 

Starting Models: experimental

Literature

Structural basis for blocking PD-1-mediated immune suppression by therapeutic antibody pembrolizumab.

Na, Z., Yeo, S.P., Bharath, S.R., Bowler, M.W., Balijkcij, E., Wang, C.I., Song, H.

(2017) Cell Res 27: 147-150

• PubMed: 27325296 
• DOI: https://doi.org/10.1038/cr.2016.77
• Primary Citation of Related Structures:  
  5JXE

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Organizational Affiliation: 

Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 120.33 kDa 
• Atom Count: 7,851 
• Modelled Residue Count: 1,043 
• Deposited Residue Count: 1,100 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A, B	114	Homo sapiens	Mutation(s): 1  Gene Names: PDCD1, PD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15116 (Homo sapiens) Explore Q15116  Go to UniProtKB:  Q15116
PHAROS:  Q15116 GTEx:  ENSG00000188389

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pembrolizumab Fab light chain	C, E [auth F]	218	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pembrolizumab Fab heavy chain	D, F [auth G]	218	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.261 
• R-Value Observed: 0.262 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.554	α = 90
b = 105.554	β = 90
c = 380.048	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Na, Z., Bharath, S.R., Song, H.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2016-09-07
  Changes: Experimental preparation
• Version 1.2: 2017-12-06
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary