MolNFT v1 · #17262 · protein

Crystal structure of CD1A in complex with a sulfatide

1ONQ · T-cell surface glycoprotein CD1A: “Crystal structure of CD1A in complex with a sulfatide”. X-ray diffraction, 3 ligands (SLF, NAG, FUC), 11 pockets (best druggability 0.86). MolNFT v1 #17262 on GenesisL1: 3D structure, binding sites…

PDB: 1ONQ
Type: protein
Length: 745 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell surface glycoprotein CD1A; Beta-2-microglobulin
UniProt: P06126, P01884
Ligands: SLF, NAG, FUC
Pockets: 11 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-cell surface glycoprotein CD1A	protein	274	28% helix, 44% strand	P06126
B, D	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P01884
C	T-cell surface glycoprotein CD1A	protein	273	28% helix, 41% strand	P06126

Ligands and binding sites

SLF · Sulfate-3-D-galactosyl-beta-1-1-N-stearoyl-D-sphingosine · ligand · 2 copies · chains A, C
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C
FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B, C

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

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	620	0.86	0.90	46	SLF
2	654	0.84	0.88	52	SLF
3	563	0.68	0.78	55	empty
4	500	0.67	0.78	54	empty
5	174	0.49	0.77	28	empty

Interfaces

3 interfaces between chains.

A–B · 1408 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1378 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 190 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 5 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

1ONQ · Crystal Structure of CD1a in Complex with a Sulfatide · the same entry in another collection · chain A against A, TM-score 1.00
P06126 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1A (P06126) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P06126
Every structure of UniProt P01884
Elsewhere: RCSB PDB 1ONQ · PDBe 1ONQ · UniProt P06126 · UniProt P01884

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