5IND

Crystal structure of HLA-B5801, a protective HLA allele for HIV-1 infection

• PDB DOI: https://doi.org/10.2210/pdb5IND/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, unidentified
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-07 Released: 2016-10-05 
• Deposition Author(s): Li, X., Wang, J.-H.
• Funding Organization(s): Ragon Institute of MGH, MIT and Harvard

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.229 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Crystal structure of HLA-B*5801, a protective HLA allele for HIV-1 infection.

Li, X., Lamothe, P.A., Ng, R., Xu, S., Teng, M., Walker, B.D., Wang, J.H.

(2016) Protein Cell 7: 761-765

• PubMed: 27638468 
• DOI: https://doi.org/10.1007/s13238-016-0309-y
• Primary Citation of Related Structures:  
  5IM7, 5INC, 5IND

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Organizational Affiliation: 

School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.

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: 89.6 kDa 
• Atom Count: 6,749 
• Modelled Residue Count: 770 
• Deposited Residue Count: 770 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B-58 alpha chain	A, C	277	Homo sapiens	Mutation(s): 0  Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889  Go to UniProtKB:  P01889
PHAROS:  P01889 GTEx:  ENSG00000234745

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	99	Homo sapiens	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GLN-ALA-SER-GLN-ASP-VAL-LYS-ASN-TRP	E, F	9	unidentified	Mutation(s): 0
UniProt
Find proteins for P04591 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04591  Go to UniProtKB:  P04591

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.229 
• R-Value Work: 0.186 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.413	α = 90
b = 82.28	β = 90
c = 157.72	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Li, X., Wang, J.-H.

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Funding Organization	Location	Grant Number
Ragon Institute of MGH, MIT and Harvard	United States	--

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary