Research workbench

CD1B in complex with phophatidylinositol

Analyse CD1B in complex with phophatidylinositol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1GZQ
Type: protein
Length: 377 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell surface glycoprotein CD1B; B2-microglobulin
UniProt: P29016, P01884
Ligands: PII, D12, TWT, NO3
Pockets: 4 · best druggability 0.87

Structure

x-ray diffraction · 2 distinct chains · 20% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-cell surface glycoprotein CD1B	protein	277	27% helix, 42% strand	P29016
B	B2-microglobulin	protein	100	0% helix, 49% strand	P01884

Ligands and binding sites

PII · 2-[(hydroxy{[(2r,3r,5s,6r)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl)oxy]-1-[(palmitoyloxy)methyl]ethyl heptadecanoate · ligand · chains A
D12 · Dodecane · ligand · chains A
TWT · Docosane · ligand · chains A
NO3 · Nitrate ion · ion · 3 copies · chains A, B

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

Pockets

4 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	819	0.87	0.90	71	PII, D12, TWT
2	337	0.64	0.80	44	empty
3	138	0.45	0.77	27	empty
4	78	0.42	0.80	15	NO3

Interfaces

1 interface between chains.

A–B · 1390 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1GZQ · CD1b in complex with Phophatidylinositol · the same entry in another collection · chain A against A, TM-score 1.00
P29016 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1B (P29016) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P29016
Every structure of UniProt P01884
Elsewhere: RCSB PDB 1GZQ · PDBe 1GZQ · UniProt P29016 · UniProt P01884

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