6VQZ | pdb_00006vqz

HLA-B*27:05 presenting an HIV-1 6mer peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

Epitope length variants balance protective immune responses and viral escape in HIV-1 infection

Pymm, P., Tenzer, S., Wee, E., Weimershaus, M., Burgevin, A., Kollnberger, S., Gerstoft, J., Josephs, T.M., Ladell, K., McLaren, J.E., Appay, V., Price, D.A., Fugger, L., Bell, J.I., Schild, H., van Endert, P., Harkiolaki, M., Iversen, A.K.

(2022) Cell Rep 38


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MHC class I antigen
A, C
276Homo sapiensMutation(s): 0 
Gene Names: HLA-B
UniProt
Find proteins for O78189 (Homo sapiens)
Explore O78189 
Go to UniProtKB:  O78189
Entity Groups  
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UniProt GroupO78189
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin
B, D
99Homo 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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
6-mer peptideE [auth G],
F		6Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04585 
Go to UniProtKB:  P04585
Entity Groups  
UniProt GroupP04585
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.495α = 90
b = 130.516β = 104.41
c = 90.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Advisory, Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary