MolNFT v1 · #90398 · protein

Crystal structure of XV19 TCR in complex with CD1D-sulfatide C24:1

4EI5 · Antigen-presenting glycoprotein CD1D1: “Crystal structure of XV19 TCR in complex with CD1D-sulfatide C24:1”. X-ray diffraction, 4 ligands (CIS, NAG, BMA), 20 pockets (best druggability 0.85). MolNFT v1 #90398 on GenesisL1: 3D…

PDB: 4EI5
Type: protein
Length: 1,613 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; VALPHA1 XV19 type II natural…
UniProt: P11609, P01887
Ligands: CIS, NAG, BMA, MAN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 8 distinct chains · 12% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antigen-presenting glycoprotein CD1D1	protein	295	26% helix, 38% strand	P11609
B	Beta-2-microglobulin	protein	98	0% helix, 50% strand	P01887
C	VALPHA1 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain)	protein	201	3% helix, 48% strand	—
D	VBETA16 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain)	protein	242	7% helix, 50% strand	—
E	Antigen-presenting glycoprotein CD1D1	protein	280	25% helix, 40% strand	P11609
F	Beta-2-microglobulin	protein	95	0% helix, 52% strand	P01887
G	VALPHA1 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain)	protein	172	3% helix, 43% strand	—
H	VBETA16 XV19 type II natural killer T cell receptor (mouse variable domain, human constant domain)	protein	230	8% helix, 49% strand	—

Ligands and binding sites

CIS · (15Z)-N-((1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-enyl)tetracos-15-enamide · ligand · 2 copies · chains A, D, E, H
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, C, E, G
BMA · beta-D-mannopyranose · sugar · 2 copies
MAN · alpha-D-mannopyranose · sugar
FLC · Citrate anion · additive · chains A, B

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

Pockets

20 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	803	0.85	0.87	86	CIS
2	781	0.85	0.87	85	CIS
3	846	0.73	0.78	87	empty
4	961	0.72	0.76	65	empty
5	452	0.65	0.78	48	empty

Interfaces

9 interfaces between chains.

C–D · 2323 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1831 Å² buried · 21 hydrogen bonds · protein-protein
A–B · 1693 Å² buried · 21 hydrogen bonds · protein-protein
E–F · 1194 Å² buried · 9 hydrogen bonds · protein-protein
E–G · 538 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

4EI5 · Crystal Structure of XV19 TCR in complex with CD1d-sulfatide C24:1 · the same entry in another collection · chain H against H, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain F against A, TM-score 0.99
P11609 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D1 (P11609) · a predicted model of the same protein · chain E against A, TM-score 0.96

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
Every structure of UniProt P01887
Elsewhere: RCSB PDB 4EI5 · PDBe 4EI5 · UniProt P11609 · UniProt P01887

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