9CGR

Structure of human MAIT A-F7 TCR in complex with human MR1-Pyridoxal

PDB DOI: https://doi.org/10.2210/pdb9CGR/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-30 Released: 2024-11-27
Deposition Author(s): Awad, W., Rossjohn, R.
Funding Organization(s): Australian Research Council (ARC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.216
R-Value Work: 0.173
R-Value Observed: 0.174

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

MR1 presents vitamin B6 related compounds for recognition by MR1-reactive T cells

Awad, W., Rossjohn, R.

(2024) Proc Natl Acad Sci U S A

Macromolecule Content

Total Structure Weight: 189.77 kDa
Atom Count: 13,293
Modelled Residue Count: 1,613
Deposited Residue Count: 1,642
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major histocompatibility complex class I-related gene protein	A, C	271	Homo sapiens	Mutation(s): 0 Gene Names: MR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q95460 (Homo sapiens) Explore Q95460 Go to UniProtKB: Q95460
PHAROS: Q95460 GTEx: ENSG00000153029
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q95460
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, F	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR TRAV1-2	D, G	204	Homo sapiens	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
TCR TRBV 6-1	E, H	246	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PXL (Subject of Investigation/LOI) Query on PXL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth C] MOL2 format, chain I [auth A] MOL2 format, chain O [auth C] mmCIF format, chain I [auth A] mmCIF format, chain O [auth C]	I [auth A], O [auth C]	3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE C₈ H₉ N O₃ RADKZDMFGJYCBB-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth C] Interactions & Density Focus chain I [auth A] Focus chain O [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain J [auth A] SDF format, chain M [auth A] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain U [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain AA [auth G] MOL2 format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain AA [auth G] mmCIF format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F]	AA [auth G] J [auth A] M [auth A] P [auth C] Q [auth C] AA [auth G], J [auth A], M [auth A], P [auth C], Q [auth C], R [auth C], U [auth C], X [auth D], Y [auth F], Z [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain J [auth A] Focus chain M [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain J [auth A] Focus chain M [auth A] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth C] Focus chain X [auth D] Focus chain Y [auth F] Focus chain Z [auth F]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth C]	K [auth A], L [auth A], S [auth C], T [auth C], V [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain BA [auth H] MOL2 format, chain BA [auth H] mmCIF format, chain BA [auth H]	BA [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Interactions & Density Focus chain BA [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain W [auth C] MOL2 format, chain N [auth A] MOL2 format, chain W [auth C] mmCIF format, chain N [auth A] mmCIF format, chain W [auth C]	N [auth A], W [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth A] Focus chain W [auth C] Interactions & Density Focus chain N [auth A] Focus chain W [auth C]