8K4T

Crystal structure of HLA-A*11:01 in complex with KRAS G12C peptide (VVVGACGVGK)

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2023-07-20 Released: 2025-01-29 
  • Deposition Author(s): Xu, Y.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.316 (Depositor), 0.317 (DCC) 
  • R-Value Work: 
    0.258 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 
    0.261 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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Literature

Crystal structure of HLA-A*11:01 in complex with KRAS G12C peptide (VVVGACGVGK)

Xu, Y.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HLA class I histocompatibility antigen, A alpha chain
A, D
276Homo sapiensMutation(s): 3 
Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens)
Explore P04439 
Go to UniProtKB:  P04439
PHAROS:  P04439
GTEx:  ENSG00000206503 
Entity Groups  
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UniProt GroupP04439
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, E
122Homo sapiensMutation(s): 0 
Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
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UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
KRAS G12C peptide (VVVGACGVGK)
C, F
10Homo sapiensMutation(s): 1 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.316 (Depositor), 0.317 (DCC) 
  • R-Value Work:  0.258 (Depositor), 0.260 (DCC) 
  • R-Value Observed: 0.261 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.708α = 105.864
b = 63.579β = 92.656
c = 75.507γ = 97.701
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Cootmodel building
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-01-29 
    • Deposition Author(s): Xu, Y.
Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2021YFA1302200

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release