6RP8 | pdb_00006rp8

Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution

• PDB DOI: https://doi.org/10.2210/pdb6RP8/pdb

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


• Deposited: 2019-05-14 Released: 2020-07-08 
• Deposition Author(s): Zhang, F., Zhou, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.267 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution

Zhang, F., Zhou, A.

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 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: 120.69 kDa 
• Atom Count: 8,177 
• Modeled Residue Count: 1,073 
• Deposited Residue Count: 1,116 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Ipilimumab heavy chain	A [auth h], C [auth H]	225	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody Ipilimumab light chain	B [auth l], D [auth L]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytotoxic T-lymphocyte protein 4	E [auth C], F [auth c]	118	Homo sapiens	Mutation(s): 0  Gene Names: CTLA4, CD152
UniProt & NIH Common Fund Data Resources
Find proteins for P16410 (Homo sapiens) Explore P16410  Go to UniProtKB:  P16410
PHAROS:  P16410 GTEx:  ENSG00000163599

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.267 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.91	α = 90
b = 129.89	β = 96.44
c = 76.91	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Zhang, F., Zhou, A.

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Advisory, Data collection, Database references, Structure summary