9AUD | pdb_00009aud

Immune receptor complex

PDB DOI: https://doi.org/10.2210/pdb9AUD/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Influenza A virus H3N2
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): No

Deposited: 2024-02-29 Released: 2025-02-05
Deposition Author(s): Chaurasia, P., Littler, D.R., La Gruta, N., Rossjohn, J.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.216 (Depositor), 0.215 (DCC)
R-Value Work:
0.183 (Depositor), 0.184 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

NP-LCK2-1TCR-MHC complex

Zhang, J.B., Chaurasia, P., Littler, D.R., La Gruta, N., Rossjohn, J.

To be published.

Macromolecule Content

Total Structure Weight: 99.14 kDa
Atom Count: 6,196
Modeled Residue Count: 783
Deposited Residue Count: 868
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class II histocompatibility antigen, A-B alpha chain	A [auth C]	188	Mus musculus	Mutation(s): 0 Gene Names: H2-Aa
UniProt
Find proteins for P14434 (Mus musculus) Explore P14434 Go to UniProtKB: P14434
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P14434
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth C]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein,H-2 class II histocompatibility antigen, A beta chain	B [auth D]	228	Influenza A virus H3N2, Mus musculus This entity is chimeric	Mutation(s): 0 Gene Names: NP, H2-Ab1, H2-iabeta
UniProt
Find proteins for O92607 (Influenza A virus H3N2) Explore O92607 Go to UniProtKB: O92607
Find proteins for P14483 (Mus musculus) Explore P14483 Go to UniProtKB: P14483
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P14483O92607
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B [auth D]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
NPLCK1-2_TCR TRAV6-5 alpha chain	C [auth A]	210	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
NPLCK1-2 TCR TRBV1 Beta chain	D [auth B]	242	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain G [auth C] MOL2 format, chain I [auth D] MOL2 format, chain G [auth C] mmCIF format, chain I [auth D] mmCIF format, chain G [auth C]	G [auth C], I [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth C] Focus chain I [auth D] Interactions & Density Focus chain G [auth C] Focus chain I [auth D]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain H [auth C] SDF format, chain J [auth D] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain H [auth C] MOL2 format, chain J [auth D] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain H [auth C] mmCIF format, chain J [auth D] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	E [auth C] F [auth C] H [auth C] J [auth D] K [auth B] E [auth C], F [auth C], H [auth C], J [auth D], K [auth B], L [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain H [auth C] Focus chain J [auth D] Focus chain K [auth B] Focus chain L [auth B]