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Crystal structure of CD1D-lipid-antigen complexed with beta-2- microglobulin, NKT15 alpha-chain and NKT15 beta-chain

Analyse Crystal structure of CD1D-lipid-antigen complexed with beta-2- microglobulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2PO6
Type: protein
Length: 1,639 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell surface glycoprotein CD1D; Beta-2-microglobulin; NKT15 alpha-chain; NKT15…
UniProt: P15813, P61769, Q6PIZ8, Q6GMR4
Ligands: AGH, NAG, BMA
Pockets: 19 · best druggability 0.87

Structure

x-ray diffraction · 7 distinct chains · 12% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-cell surface glycoprotein CD1D	protein	275	25% helix, 37% strand	P15813
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	NKT15 alpha-chain	protein	203	1% helix, 44% strand	Q6PIZ8
D, H	NKT15 beta-chain	protein	244	7% helix, 49% strand	Q6GMR4
E	T-cell surface glycoprotein CD1D	protein	272	24% helix, 39% strand	P15813
F	Beta-2-microglobulin	protein	98	0% helix, 52% strand	P61769
G	NKT15 alpha-chain	protein	204	3% helix, 45% strand	Q6PIZ8

Ligands and binding sites

AGH · N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}hexacosanamide · ligand · 2 copies · chains A, C, E, G
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains E, A
BMA · beta-D-mannopyranose · sugar

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	746	0.87	0.90	82	AGH
2	830	0.86	0.88	85	AGH
3	976	0.75	0.78	81	empty
4	1090	0.72	0.76	100	empty
5	973	0.71	0.75	80	empty

Interfaces

11 interfaces between chains.

G–H · 2460 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 2305 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 1425 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1370 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 460 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation, glycosylation).

Compared structures

2PO6 · Crystal structure of CD1d-lipid-antigen complexed with Beta-2-Microglobulin, NKT15… · the same entry in another collection · chain H against H, TM-score 1.00
P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain E against A, TM-score 0.99
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain F 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 P15813
Every structure of UniProt P61769
Every structure of UniProt Q6PIZ8
Every structure of UniProt Q6GMR4
Elsewhere: RCSB PDB 2PO6 · PDBe 2PO6 · UniProt P15813 · UniProt P61769 · UniProt Q6PIZ8 · UniProt Q6GMR4

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