Macromolecule Content

Total Structure Weight: 45.31 kDa
Atom Count: 3485
Residue Count: 385
Unique protein chains: 3

6VB7

HLA-B*15:02 complexed with a synthetic peptide

DOI: 10.2210/pdb6VB7/pdb

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

Deposited: 2019-12-18 Released: 2020-11-25
Deposition Author(s): Schutte, R.J., Li, D., Ostrov, D.A.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.257
R-Value Work: 0.194
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Literature

HLA-B*15:02 complexed with a synthetic peptide

Schutte, R.J., Li, D., Ostrov, D.A.

To be published.

Macromolecules

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(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-B
Find proteins for F4NBQ8 (Homo sapiens) Explore F4NBQ8 Go to UniProtKB: F4NBQ8
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
NIH Common Fund Data Resources
PHAROS P61769 GTEx ENSG00000166710
Protein Feature View Expand
Reference Sequence

Find similar proteins by: Sequence | Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic peptide THR-VAL-ARG-ALA-SER-GLY-HIS-SER-TYR	C	9	synthetic construct	Mutation(s): 0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] SDF format, chain H [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain H [A]	A	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain I [A] SDF format, chain K [B] MOL2 format, chain I [A] MOL2 format, chain K [B]	A, B	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [A] MOL2 format, chain D [A] MOL2 format, chain E [A]	A	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [B] MOL2 format, chain J [B]	B	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.257
R-Value Work: 0.194
R-Value Observed: 0.198
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.906	α = 90
b = 81.522	β = 90
c = 110.15	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2019-12-18
Released Date: 2020-11-25

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R01AI103348-01

Revision History

Version 1.0: 2020-11-25
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.