7PDY

A viral peptide from Marek's disease virus bound to chicken MHC-II molecule

PDB DOI: https://doi.org/10.2210/pdb7PDY/pdb

Classification: IMMUNE SYSTEM
Organism(s): Gallus gallus, Marek's disease herpesvirus (strain MD11/75C/R2)
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2021-08-09 Released: 2022-08-24
Deposition Author(s): Goryanin, A., Cook, A.G., Kaufman, J., Halabi, S.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.216 (Depositor), 0.220 (DCC)
R-Value Observed:
0.217 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Viral peptide bound to chicken MHC-II molecule

Goryanin, A., Cook, A.G., Kaufman, J., Halabi, S.

To be published.

Macromolecule Content

Total Structure Weight: 143.79 kDa
Atom Count: 9,525
Modelled Residue Count: 1,165
Deposited Residue Count: 1,248
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class II alpha chain	A, C, E	191	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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
38 kDa phosphoprotein,MHC class II beta chain	B, D, F	225	Marek's disease herpesvirus (strain MD11/75C/R2), Gallus gallus This entity is chimeric	Mutation(s): 0 Gene Names: PP38
UniProt
Find proteins for P68348 (Gallid herpesvirus 2 (strain MD11/75C/R2)) Explore P68348 Go to UniProtKB: P68348
Find proteins for Q4U5Z9 (Gallus gallus) Explore Q4U5Z9 Go to UniProtKB: Q4U5Z9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	Q4U5Z9P68348
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain F
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N/A	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain X [auth F] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth F] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth F]	H [auth A], Q [auth C], U [auth D], X [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth F] Interactions & Density Focus chain H [auth A] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth F]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B]	L [auth A], O [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Interactions & Density Focus chain L [auth A] Focus chain O [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain W [auth E] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth E] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain W [auth E]	I [auth A], K [auth A], M [auth B], T [auth C], W [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain W [auth E] Interactions & Density Focus chain I [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain T [auth C] Focus chain W [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth F] SDF format, chain P [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth F] MOL2 format, chain P [auth B] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth F] mmCIF format, chain P [auth B]	J [auth A] N [auth B] P [auth B] R [auth C] S [auth C] J [auth A], N [auth B], P [auth B], R [auth C], S [auth C], V [auth D], Y [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth F] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth F]