5WT9

Complex structure of PD-1 and nivolumab-Fab

• PDB DOI: https://doi.org/10.2210/pdb5WT9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2016-12-10 Released: 2017-02-15 
• Deposition Author(s): Tan, S., Zhang, H., Chai, Y., Song, H., Tong, Z., Wang, Q., Qi, J., Wong, G., Zhu, X., Liu, W.J., Gao, S., Wang, Z., Shi, Y., Yang, F., Gao, G.F., Yan, J.
• Funding Organization(s): Scientific Research and Development of China, National Natural Science Foundation of China, Chinese Academy of Sciences, China National Grand S&T Special Project

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.228 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 67.54 kDa 
• Atom Count: 4,391 
• Modelled Residue Count: 533 
• Deposited Residue Count: 610 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain of Nivolumab	A [auth H]	220	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain of Nivolumab	B [auth L]	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	C [auth G]	173	Homo sapiens	Mutation(s): 0  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

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth A]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.228 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.527	α = 90
b = 108.527	β = 90
c = 145.423	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-15 
Deposition Author(s): Tan, S., Zhang, H., Chai, Y., Song, H., Tong, Z., Wang, Q., Qi, J., Wong, G., Zhu, X., Liu, W.J., Gao, S., Wang, Z., Shi, Y., Yang, F., Gao, G.F., Yan, J.

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Funding Organization	Location	Grant Number
Scientific Research and Development of China	China	2016YFC1200300
National Natural Science Foundation of China	China	31390432
National Natural Science Foundation of China	China	31500722
Chinese Academy of Sciences	China	153211KYSB20160001
China National Grand S&T Special Project	China	2013ZX10004608-002
National Natural Science Foundation of China	China	81321063

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary