MolNFT v1 · #78603 · protein

Crystal structure of human autoreactive-VALPHA24 nkt TCR in complex with CD1D-beta-galactosylceramide

3SDX · Antigen-presenting glycoprotein CD1D: “Crystal structure of human autoreactive-VALPHA24 nkt TCR in complex with CD1D-beta-galactosylceramide”. X-ray diffraction, 1 ligand (GCY), 19 pockets (best druggability 0.88). MolNFT v1 #78603…

PDB: 3SDX
Type: protein
Length: 1,611 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen-presenting glycoprotein CD1D; Beta-2-microglobulin; Nkt TCR VALPHA24 chain; Nkt…
UniProt: P15813, P61769
Ligands: GCY
Pockets: 19 · best druggability 0.88

Structure

x-ray diffraction · 6 distinct chains · 13% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antigen-presenting glycoprotein CD1D	protein	275	22% helix, 39% strand	P15813
B, D	Beta-2-microglobulin	protein	97	0% helix, 51% strand	P61769
E, G	Nkt TCR VALPHA24 chain	protein	196	4% helix, 46% strand	—
F	Nkt TCR autoreactive-VBETA11 chain	protein	242	6% helix, 50% strand	—
C	Antigen-presenting glycoprotein CD1D	protein	268	26% helix, 38% strand	P15813
H	Nkt TCR autoreactive-VBETA11 chain	protein	240	6% helix, 51% strand	—

Ligands and binding sites

GCY · N-[(2S,3R)-1-(beta-D-galactopyranosyloxy)-3-hydroxyoctadec-4-en-2-yl]tetracosanamide · ligand · 2 copies · chains A, E, G, C

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

Pockets

19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	840	0.88	0.90	75	GCY
2	958	0.87	0.88	90	GCY
3	907	0.75	0.78	70	empty
4	969	0.71	0.75	79	empty
5	874	0.69	0.75	70	empty

Interfaces

11 interfaces between chains.

E–F · 2064 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 2039 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1173 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1133 Å² buried · 15 hydrogen bonds · protein-protein
G–C · 520 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

3SDX · Crystal structure of human autoreactive-Valpha24 NKT TCR in complex with… · 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 C 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 B 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 P15813
Every structure of UniProt P61769
Elsewhere: RCSB PDB 3SDX · PDBe 3SDX · UniProt P15813 · UniProt P61769

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