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Ternary crystal structure of the human nkt TCR-CD1D-C20:2 complex

Analyse Ternary crystal structure of the human nkt TCR-CD1D-C20:2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VWJ
Type: protein
Length: 783 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen-presenting glycoprotein CD1D; Beta-2-microglobulin; NKT15 T cell receptor…
UniProt: P15813, P61769
Ligands: DB3, NAG, MG
Pockets: 9 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antigen-presenting glycoprotein CD1D	protein	252	24% helix, 36% strand	P15813
B	Beta-2-microglobulin	protein	97	0% helix, 47% strand	P61769
C	NKT15 T cell receptor alpha-chain	protein	193	2% helix, 44% strand	—
D	NKT15 T cell receptor beta-chain	protein	241	6% helix, 49% strand	—

Ligands and binding sites

DB3 · (11Z,14E)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]icosa-11,14-dienamide · ligand · chains A, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
MG · Magnesium ion · metal · chains A, D

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	905	0.87	0.89	83	DB3
2	628	0.65	0.75	80	empty
3	386	0.62	0.77	39	empty
4	191	0.54	0.79	33	empty
5	100	0.52	0.82	20	empty

Interfaces

4 interfaces between chains.

C–D · 1932 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 1154 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 474 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 330 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

3VWJ · Ternary crystal structure of the human NKT TCR-CD1d-C20:2 complex · the same entry in another collection · chain A against A, TM-score 1.00
P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain A against A, TM-score 0.98
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P15813
Every structure of UniProt P61769
Elsewhere: RCSB PDB 3VWJ · PDBe 3VWJ · UniProt P15813 · UniProt P61769

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