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Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex

Analyse Crystal structure of the mCD1d/xxs (JJ304) /iNKTCR ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MJI
Type: protein
Length: 809 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.3
Source: Homo sapiens; Mus musculus
Molecule: T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha…
UniProt: A0A0B4J1J9, K7N5M3, A2NTY6, A0N8J3, A0A5B9, A0A0R4J090, P01887
Ligands: JTD, NAG, BMA, MAN, FUC, NA
Pockets: 9 · best druggability 0.86

Structure

x-ray diffraction · resolution 2.3 · 4 distinct chains · 12% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	T cell receptor alpha variable 11,T cell receptor alpha joining 18,Human nkt tcr alpha chain, CHIMERIC PROTEIN	protein	203	5% helix, 47% strand	A0A0B4J1J9, K7N5M3
D	Beta-chain,Tcell receptor chain,T cell receptor beta constant 2	protein	239	6% helix, 49% strand	A2NTY6, A0N8J3, A0A5B9
A	Antigen-presenting glycoprotein CD1d1	protein	270	27% helix, 41% strand	A0A0R4J090
B	Beta-2-microglobulin	protein	97	0% helix, 51% strand	P01887

Ligands and binding sites

JTD · N-[(2S,3S,4R)-1-{[4-O-(cyclopropylmethyl)-alpha-D-galactopyranosyl]oxy}-3,4-dihydroxyoctadecan-2-yl]hexacosanamide · ligand · chains C, A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
BMA · beta-D-mannopyranose · sugar
MAN · alpha-D-mannopyranose · sugar
FUC · alpha-L-fucopyranose · sugar · chains A
NA · Sodium ion · metal · 2 copies · chains C, D
GOL · Glycerol · additive · 6 copies · chains C, D, A, B

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	940	0.86	0.87	79	JTD
2	901	0.68	0.74	67	empty
3	459	0.65	0.78	51	GOL
4	197	0.48	0.75	30	empty
5	130	0.46	0.77	24	empty

Interfaces

4 interfaces between chains.

C–D · 2111 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1182 Å² buried · 10 hydrogen bonds · protein-protein
C–A · 479 Å² buried · 8 hydrogen bonds · protein-protein
D–A · 365 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

6MJI · Crystal structure of the MCD1D/XXS (JJ304) /inktcr ternary complex · the same entry in another collection · chain A against A, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain B against A, TM-score 0.98
A0A5B9 · AlphaFold monomer V2.0 prediction for T cell receptor beta constant 2 (A0A5B9) · a predicted model of the same protein · chain D against A, TM-score 0.53

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 A0A0B4J1J9
Every structure of UniProt K7N5M3
Every structure of UniProt A2NTY6
Every structure of UniProt A0N8J3
Every structure of UniProt A0A5B9
Every structure of UniProt A0A0R4J090
Every structure of UniProt P01887
Elsewhere: RCSB PDB 6MJI · PDBe 6MJI · UniProt A0A0B4J1J9 · UniProt K7N5M3 · UniProt A2NTY6 · UniProt A0N8J3 · UniProt A0A5B9 · UniProt A0A0R4J090 · UniProt P01887

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