6J15

Complex structure of GY-5 Fab and PD-1

• PDB DOI: https://doi.org/10.2210/pdb6J15/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Insect cell expression vector pTIE1
• Mutation(s): No 


• Deposited: 2018-12-27 Released: 2019-11-06 
• Deposition Author(s): Chen, D., Tan, S., Zhang, H., Wang, H., Chai, Y., Qi, J., Yan, J., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

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 Evidence: surface plasmon resonance

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: 124.3 kDa 
• Atom Count: 8,342 
• Modelled Residue Count: 1,056 
• Deposited Residue Count: 1,110 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A [auth C], B [auth D]	120	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GY-5 heavy chain Fab	C [auth H], E [auth A]	219	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GY-5 light chain Fab	D [auth L], F [auth B]	216	Mus musculus	Mutation(s): 0

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	G [auth E]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F]	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G47477HI GlyCosmos:  G47477HI GlyGen:  G47477HI

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth C], J [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.277 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.595	α = 90
b = 64.347	β = 98.04
c = 151.481	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Chen, D., Tan, S., Zhang, H., Wang, H., Chai, Y., Qi, J., Yan, J., Gao, G.F.

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary