3V5D | pdb_00003v5d

HLA-A2.1 KVAELVHFL

• PDB DOI: https://doi.org/10.2210/pdb3V5D/pdb

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


• Deposited: 2011-12-16 Released: 2012-12-05 
• Deposition Author(s): Collins, E.J., Lee, H.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.264 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Prediction of conformation and immunogenicity of peptides bound to MHC molecules

Collins, E.J., Lee, H.Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 89.58 kDa 
• Atom Count: 6,807 
• Modeled Residue Count: 768 
• Deposited Residue Count: 768 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A, D	275	Homo sapiens	Mutation(s): 0  Gene Names: HLA*0201, 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	100	Homo sapiens	Mutation(s): 0  Gene Names: B2M, beta-2-microglobulin, 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV peptide KVAELVHFL	C, F	9	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for E0YFW1 (Human immunodeficiency virus type 1) Explore E0YFW1  Go to UniProtKB:  E0YFW1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.264 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.233	α = 90
b = 90.493	β = 90.06
c = 79.967	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Collins, E.J., Lee, H.Y.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary