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Mycobacterial lipoglycan presentation by CD1D

Analyse Mycobacterial lipoglycan presentation by CD1D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2GAZ
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
Ligands: XPX, NAG, MAN, BMA
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-cell surface glycoprotein CD1D1	protein	269	25% helix, 43% strand	P11609
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	—

Ligands and binding sites

XPX · (2R)-3-[(hydroxy{[(2r,3r,5s,6r)-3,4,5-trihydroxy-2,6-bis(alpha-D-mannopyranosyloxy)cyclohexyl]oxy}phosphoryl)oxy]propan E-1,2-diyl dihexadecanoate · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 2 copies
BMA · beta-D-mannopyranose · sugar

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	655	0.84	0.88	58	XPX
2	409	0.64	0.78	52	empty
3	139	0.48	0.78	28	empty
4	138	0.44	0.76	19	empty

Interfaces

1 interface between chains.

A–B · 1301 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2GAZ · Mycobacterial lipoglycan presentation by CD1d · 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 0.99

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 P11609
Elsewhere: RCSB PDB 2GAZ · PDBe 2GAZ · UniProt P11609

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