9D95 | pdb_00009d95

TCR - peptide - HLA complex

PDB DOI: https://doi.org/10.2210/pdb9D95/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, human gammaherpesvirus 4
Expression System: Escherichia coli, synthetic construct, Homo sapiens
Mutation(s): No

Deposited: 2024-08-21 Released: 2025-09-03
Deposition Author(s): Zhu, S., Petersen, J., Rossjohn, J.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.235 (Depositor), 0.234 (DCC)
R-Value Work:
0.202 (Depositor), 0.202 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

T cell recognition of a viral antigen

Zhu, S., Petersen, J., Rossjohn, J.

To be published.

Macromolecule Content

Total Structure Weight: 394.1 kDa
Atom Count: 25,533
Modeled Residue Count: 3,250
Deposited Residue Count: 3,424
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, F, K, P	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-B, HLA-DRB1
UniProt
Find proteins for E5FQ58 (Homo sapiens) Explore E5FQ58 Go to UniProtKB: E5FQ58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E5FQ58
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, G, L, Q	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
Epstein-Barr nuclear antigen 2	C, H, M, R	10	human gammaherpesvirus 4	Mutation(s): 0 Gene Names: EBNA2, BYRF1
UniProt
Find proteins for P12978 (Epstein-Barr virus (strain B95-8)) Explore P12978 Go to UniProtKB: P12978
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12978
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha chain	D, I, N, S	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain D Focus chain I Focus chain N Focus chain S
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta chain	E, J, O, T	256	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain EA [auth K] SDF format, chain MA [auth P] SDF format, chain Y [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain EA [auth K] MOL2 format, chain MA [auth P] MOL2 format, chain Y [auth D] mmCIF format, chain AA [auth F] mmCIF format, chain EA [auth K] mmCIF format, chain MA [auth P] mmCIF format, chain Y [auth D]	AA [auth F], EA [auth K], MA [auth P], Y [auth D]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth K] Focus chain MA [auth P] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth K] Focus chain MA [auth P] Focus chain Y [auth D]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain DA [auth I] SDF format, chain HA [auth N] SDF format, chain IA [auth N] SDF format, chain JA [auth N] SDF format, chain KA [auth N] SDF format, chain LA [auth N] SDF format, chain OA [auth S] SDF format, chain PA [auth S] SDF format, chain QA [auth S] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth D] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth I] MOL2 format, chain HA [auth N] MOL2 format, chain IA [auth N] MOL2 format, chain JA [auth N] MOL2 format, chain KA [auth N] MOL2 format, chain LA [auth N] MOL2 format, chain OA [auth S] MOL2 format, chain PA [auth S] MOL2 format, chain QA [auth S] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth D] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth I] mmCIF format, chain HA [auth N] mmCIF format, chain IA [auth N] mmCIF format, chain JA [auth N] mmCIF format, chain KA [auth N] mmCIF format, chain LA [auth N] mmCIF format, chain OA [auth S] mmCIF format, chain PA [auth S] mmCIF format, chain QA [auth S] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth D]	CA [auth I] DA [auth I] HA [auth N] IA [auth N] JA [auth N] CA [auth I], DA [auth I], HA [auth N], IA [auth N], JA [auth N], KA [auth N], LA [auth N], OA [auth S], PA [auth S], QA [auth S], V [auth D], W [auth D], X [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth I] Focus chain DA [auth I] Focus chain HA [auth N] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain QA [auth S] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth I] Focus chain DA [auth I] Focus chain HA [auth N] Focus chain IA [auth N] Focus chain JA [auth N] Focus chain KA [auth N] Focus chain LA [auth N] Focus chain OA [auth S] Focus chain PA [auth S] Focus chain QA [auth S] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain FA [auth K] SDF format, chain GA [auth K] SDF format, chain NA [auth P] SDF format, chain U [auth A] MOL2 format, chain BA [auth F] MOL2 format, chain FA [auth K] MOL2 format, chain GA [auth K] MOL2 format, chain NA [auth P] MOL2 format, chain U [auth A] mmCIF format, chain BA [auth F] mmCIF format, chain FA [auth K] mmCIF format, chain GA [auth K] mmCIF format, chain NA [auth P] mmCIF format, chain U [auth A]	BA [auth F], FA [auth K], GA [auth K], NA [auth P], U [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth F] Focus chain FA [auth K] Focus chain GA [auth K] Focus chain NA [auth P] Focus chain U [auth A] Interactions & Density Focus chain BA [auth F] Focus chain FA [auth K] Focus chain GA [auth K] Focus chain NA [auth P] Focus chain U [auth A]