Macromolecule Content

Total Structure Weight: 45.39 kDa
Atom Count: 4039
Residue Count: 385
Unique protein chains: 3

6Y28

Crystal structure of HLA-B2705 complexed with the nona-peptide mE

DOI: 10.2210/pdb6Y28/pdb

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

Deposited: 2020-02-15 Released: 2020-12-23
Deposition Author(s): Loll, B., Rueckert, C., Ziegler, B.-U., Ziegler, A.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.236
R-Value Work: 0.185
R-Value Observed: 0.187

wwPDB Validation 3D Report Full Report

Literature

A CENTRAL PEPTIDE RESIDUE CAN CONTROL MHC POLYMORPHISM-DEPENDENT ANTIGEN PRESENTATION

Loll, B., Rueckert, C., Ziegler, B.-U., Ziegler, 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 A3F718 (Homo sapiens) Explore A3F718 Go to UniProtKB: A3F718
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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
GLY-ARG-LEU-ASN-GLU-PRO-ILE-LYS-VAL	C	9	synthetic construct	Mutation(s): 0
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [A] SDF format, chain F [A] SDF format, chain G [A] SDF format, chain H [B] SDF format, chain I [C] MOL2 format, chain D [A] MOL2 format, chain E [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain H [B] MOL2 format, chain I [C]	A, B, C	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.236
R-Value Work: 0.185
R-Value Observed: 0.187
Space Group: P 2₁ 2₁ 2₁
Diffraction Data DOI: 10.18430/m36y28 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.031	α = 90
b = 83.057	β = 90
c = 110.941	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
DNA	data collection

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-02-15
Released Date: 2020-12-23

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SfB 449

Revision History

Version 1.0: 2020-12-23
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.