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

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

PDB: 3ARF
Type: protein
Length: 830 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Nkt VALPHA14-JALPHA18,NKT…
UniProt: P11609, P01887
Ligands: DB3, NAG
Pockets: 8 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antigen-presenting glycoprotein CD1D1	protein	293	27% helix, 38% strand	P11609
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01887
C	Nkt VALPHA14-JALPHA18,NKT VALPHA14-JALPHA18	protein	203	3% helix, 46% strand	—
D	VBETA8.2,VBETA8.2	protein	235	6% helix, 48% 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 · 6 copies · chains A

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

Pockets

8 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	856	0.87	0.88	73	DB3
2	932	0.70	0.75	76	empty
3	362	0.64	0.79	41	empty
4	184	0.49	0.76	27	empty
5	170	0.49	0.77	25	empty

Interfaces

4 interfaces between chains.

C–D · 2027 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1749 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 477 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 187 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3ARF · Ternary crystal structure of the mouse NKT TCR-CD1d-C20:2 · 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
P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P11609
Every structure of UniProt P01887
Elsewhere: RCSB PDB 3ARF · PDBe 3ARF · UniProt P11609 · UniProt P01887

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