MolNFT v1 · #160818 · protein

Structure of human mait a-F7 TCR in complex with human MR1-DB28

6PVC · Major histocompatibility complex class I-related gene…: “Structure of human mait a-F7 TCR in complex with human MR1-DB28”. X-ray diffraction, 2 ligands (P1J, NA), 18 pockets (best druggability 0.82). MolNFT v1 #160818 on GenesisL1…

PDB: 6PVC
Type: protein
Length: 1,607 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major histocompatibility complex class I-related gene protein; Beta-2-microglobulin…
UniProt: Q95460, P61769
Ligands: P1J, NA
Pockets: 18 · best druggability 0.82

Structure

x-ray diffraction · 7 distinct chains · 13% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major histocompatibility complex class I-related gene protein	protein	265	29% helix, 40% strand	Q95460
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P61769
C	Major histocompatibility complex class I-related gene protein	protein	267	27% helix, 41% strand	Q95460
D	Beta-2-microglobulin	protein	100	0% helix, 51% strand	P61769
E	Human TCR alpha chain	protein	192	3% helix, 47% strand	—
F, H	Human TCR beta chain	protein	242	7% helix, 51% strand	—
G	Human TCR alpha chain	protein	201	5% helix, 45% strand	—

Ligands and binding sites

P1J · N-(2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carbonyl)-beta-alanine · ligand · 2 copies · chains A, G, C, E
NA · Sodium ion · metal · chains D
GOL · Glycerol · additive · 2 copies · chains A, D
ACT · Acetate ion · additive · chains H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	866	0.82	0.84	96	empty
2	284	0.74	0.87	40	P1J
3	366	0.73	0.84	42	P1J
4	1056	0.72	0.76	76	empty
5	1083	0.71	0.75	85	empty

Interfaces

12 interfaces between chains.

E–F · 2032 Å² buried · 21 hydrogen bonds · protein-protein
G–H · 1989 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1332 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1253 Å² buried · 16 hydrogen bonds · protein-protein
C–H · 887 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

6PVC · Structure of human MAIT A-F7 TCR in complex with human MR1-DB28 · the same entry in another collection · chain H against H, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q95460
Every structure of UniProt P61769
Elsewhere: RCSB PDB 6PVC · PDBe 6PVC · UniProt Q95460 · UniProt P61769

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