5JXE | pdb_00005jxe

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 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.261 (Depositor), 0.262 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

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 Related Structures: 
  5JXE

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Organizational Affiliation: 
• Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore.
Singapore Immunology Network, 8a Biomedical Grove, Singapore 138648, Singapore.
European Molecular Biology Laboratory, Grenoble Outstation, 71 avenue des Martyrs, CS 90181 F-38042 Grenoble, France.
Unit of Virus Host-Cell Interactions, Univ. Grenoble Alpes-EMBL-CNRS, 71 avenue des Martyrs, CS 90181 F-38042 Grenoble, France.
Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, 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 
• Modeled 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 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.261 (Depositor), 0.262 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

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