6Y27 | pdb_00006y27

Crystal structure of HLA-B2709 complexed with the nona-peptide mA

PDB DOI: https://doi.org/10.2210/pdb6Y27/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: 1.38 Å
R-Value Free:
0.194 (Depositor), 0.195 (DCC)
R-Value Work:
0.158 (Depositor), 0.161 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

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

Loll, B., Rueckert, C., Ziegler, B.-U., Ziegler, A.

To be published.

Macromolecule Content

Total Structure Weight: 45.11 kDa
Atom Count: 4,089
Modeled Residue Count: 385
Deposited Residue Count: 385
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphocyte antigen HLA-B27	A	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-B
UniProt
Find proteins for A0A2R7Z5J3 (Homo sapiens) Explore A0A2R7Z5J3 Go to UniProtKB: A0A2R7Z5J3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2R7Z5J3
Sequence Annotations Expand
Reference Sequence

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| 3D 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
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
mA	C	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free: 0.194 (Depositor), 0.195 (DCC)
R-Value Work: 0.158 (Depositor), 0.161 (DCC)
R-Value Observed: 0.160 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.06	α = 90
b = 82.72	β = 90
c = 110.31	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

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-23

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2020-12-23
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary