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 
- 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
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 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Heavy Chain of Nivolumab | A [auth H] | 220 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Light Chain of Nivolumab | B [auth L] | 217 | Homo sapiens | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
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  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q15116 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 Name | Purpose |
---|---|
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHASER | phasing |
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.
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 (Full details and data files)
- 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