3V5K | pdb_00003v5k

HLA2.1 KVAELVWFL

• PDB DOI: https://doi.org/10.2210/pdb3V5K/pdb

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


• Deposited: 2011-12-16 Released: 2012-12-19 
• Deposition Author(s): Collins, E.J., Lee, H.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 
  0.228 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Prediction of Immunogenicity of altered-peptide ligands to HIV bound to MHC

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: 89.77 kDa 
• Atom Count: 6,621 
• 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-based altered-peptide ligand KVAELVWFL	C, F	9	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for E0YFW1 (Human immunodeficiency virus type 1) Explore E0YFW1  Go to UniProtKB:  E0YFW1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free:  0.228 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.773	α = 90
b = 87.078	β = 90.04
c = 79.683	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Collins, E.J., Lee, H.Y.

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary