6ZWA | pdb_00006zwa

CLIP peptide bound to chicken MHC class II molecule (BL-2) from B19 haplotype

PDB DOI: https://doi.org/10.2210/pdb6ZWA/pdb

Classification: IMMUNE SYSTEM
Organism(s): Gallus gallus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2020-07-28 Released: 2021-08-11
Deposition Author(s): Halabi, S., Brear, P., Kaufman, J.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.252 (Depositor), 0.260 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.218 (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

CLIP peptide bound to chicken MHC class II BL-2 from B19 haplotype

Halabi, S., Kaufman, J.

To be published.

Macromolecule Content

Total Structure Weight: 45.76 kDa
Atom Count: 3,212
Modeled Residue Count: 376
Deposited Residue Count: 402
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II alpha chain	A	183	Gallus gallus	Mutation(s): 0 Gene Names: B-LA
UniProt
Find proteins for Q4U5Z6 (Gallus gallus) Explore Q4U5Z6 Go to UniProtKB: Q4U5Z6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4U5Z6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Invariant chain isoform p41,MHC class II beta chain 2	B	219	Gallus gallus	Mutation(s): 0 Gene Names: Ii, CD74, BLB2
UniProt
Find proteins for A5HUL4 (Gallus gallus) Explore A5HUL4 Go to UniProtKB: A5HUL4
Find proteins for Q6J613 (Gallus gallus) Explore Q6J613 Go to UniProtKB: Q6J613
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q6J613A5HUL4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.252 (Depositor), 0.260 (DCC)
R-Value Work: 0.216 (Depositor), 0.220 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.863	α = 90
b = 60.536	β = 107.88
c = 53.855	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-08-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	110106/Z/15/Z

Revision History (Full details and data files)

Version 1.0: 2021-08-11
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.