MolNFT v1 · #65081 · protein

Structure of mouse CD1D in complex with C6PH

3GML · T-cell surface glycoprotein CD1D1: “Structure of mouse CD1D in complex with C6PH”. X-ray diffraction, 6 ligands (C6Q, PLM, NAG), 3 pockets (best druggability 0.85). MolNFT v1 #65081 on GenesisL1: 3D structure, binding sites and…

PDB: 3GML
Type: protein
Length: 367 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell surface glycoprotein CD1D1; Beta-2 microglobulin
UniProt: P11609, Q91XJ8
Ligands: C6Q, PLM, NAG, MAN, BMA, FUC
Pockets: 3 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-cell surface glycoprotein CD1D1	protein	268	27% helix, 41% strand	P11609
B	Beta-2 microglobulin	protein	99	0% helix, 49% strand	Q91XJ8

Ligands and binding sites

C6Q · N-{(1S,2S,3R)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}-6-phenylhexanamide · ligand · chains A
PLM · Palmitic acid · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 4 copies
BMA · beta-D-mannopyranose · sugar · 2 copies
FUC · alpha-L-fucopyranose · sugar · chains A
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	668	0.85	0.88	59	C6Q, PLM
2	508	0.66	0.77	56	EDO
3	199	0.46	0.74	28	empty

Interfaces

1 interface between chains.

A–B · 1202 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3GML · Structure of mouse CD1d in complex with C6Ph · the same entry in another collection · chain A against A, TM-score 1.00
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 0.98

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 P11609
Every structure of UniProt Q91XJ8
Elsewhere: RCSB PDB 3GML · PDBe 3GML · UniProt P11609 · UniProt Q91XJ8

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