5XS3

Crystal structure of HLA Class I antigen

PDB DOI: https://doi.org/10.2210/pdb5XS3/pdb

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

Deposited: 2017-06-12 Released: 2017-09-13
Deposition Author(s): Wei, P.C., Yang, Y., Liu, Z.X., Luo, Z.Q., Tu, W.Y., Han, J.Y., Deng, Y.H., Yin, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.272
R-Value Work: 0.214
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Characterization of Autoantigen Presentation by HLA-C*06:02 in Psoriasis

Wei, P., Yang, Y., Liu, Z., Luo, Z., Tu, W., Han, J., Deng, Y., Yin, L.

(2017) J Invest Dermatol 137: 2238-2241

PubMed: 28655516 Search on PubMed
DOI: https://doi.org/10.1016/j.jid.2017.05.036
Primary Citation of Related Structures:
5XS3

Organizational Affiliation

State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, Department of Biochemistry and Molecular Biology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China.

Macromolecule Content

Total Structure Weight: 44.51 kDa
Atom Count: 3,134
Modelled Residue Count: 378
Deposited Residue Count: 380
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy Chain	A	273	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light Chain	B	98	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
P	C	9	Homo sapiens	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.272
R-Value Work: 0.214
R-Value Observed: 0.220
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.21	α = 90
b = 81.1	β = 90
c = 117.19	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-09-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-09-13
Type: Initial release
Version 1.1: 2017-10-11
Changes: Database references
Version 1.2: 2023-11-22
Changes: Advisory, Data collection, Database references, Refinement description