8GY5 | pdb_00008gy5

High-resolution structure of the cemiplimab Fab in complex with PD-1

• PDB DOI: https://doi.org/10.2210/pdb8GY5/pdb

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


• Deposited: 2022-09-21 Released: 2023-10-04 
• Deposition Author(s): Heo, Y.-S., Jeong, T.J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

High-resolution structure of the cemiplimab Fab in complex with PD-1

Heo, Y.-S., Jeong, T.J.

To be published.

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: gel filtration

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 123.7 kDa 
• Atom Count: 8,854 
• Modeled Residue Count: 1,074 
• Deposited Residue Count: 1,136 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain	A, D [auth H]	229	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain	B, E [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	C [auth Q], F [auth P]	125	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.06	α = 105.73
b = 62.96	β = 98
c = 81.29	γ = 92.44

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Heo, Y.-S., Jeong, T.J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary