MolNFT v1 · #167008 · protein

Crystal structure of human CD1D presenting alpha-galactosylceramide in complex with NKT12 TCR and vhh nanobody 1D12

6V80 · Antigen-presenting glycoprotein CD1D: “Crystal structure of human CD1D presenting alpha-galactosylceramide in complex with NKT12 TCR and vhh…”. X-ray diffraction, 2 ligands (AGH, NAG), 20 pockets (best druggability 0.89). MolNFT v1…

PDB: 6V80
Type: protein
Length: 1,827 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen-presenting glycoprotein CD1D; Beta-2-microglobulin; T cell receptor alpha…
UniProt: P15813, P61769, A0A0B4J240, K7N5M3, K7N5M4
Ligands: AGH, NAG
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 10 distinct chains · 10% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antigen-presenting glycoprotein CD1D	protein	274	28% helix, 39% strand	P15813
B	Beta-2-microglobulin	protein	98	0% helix, 45% strand	P61769
C	T cell receptor alpha variable 10, nkt TCR alpha chain fusion	protein	198	2% helix, 43% strand	A0A0B4J240, K7N5M3
D	Nkt TCR beta chain	protein	240	8% helix, 40% strand	K7N5M4
E	Nanobody vhh ID12	protein	117	5% helix, 41% strand	—
F	Antigen-presenting glycoprotein CD1D	protein	270	23% helix, 39% strand	P15813
G	Beta-2-microglobulin	protein	94	0% helix, 35% strand	P61769
H	T cell receptor alpha variable 10, nkt TCR alpha chain fusion	protein	181	2% helix, 43% strand	A0A0B4J240, K7N5M3
I	Nkt TCR beta chain	protein	237	8% helix, 40% strand	K7N5M4
J	Nanobody vhh ID12	protein	118	0% helix, 46% strand	—

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, F, H, J
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1051	0.89	0.91	90	AGH
2	1200	0.89	0.90	106	AGH
3	978	0.77	0.79	116	empty
4	223	0.71	0.87	33	empty
5	844	0.70	0.76	85	empty

Interfaces

15 interfaces between chains.

C–D · 1898 Å² buried · 16 hydrogen bonds · protein-protein
H–I · 1635 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1257 Å² buried · 20 hydrogen bonds · protein-protein
F–G · 1197 Å² buried · 9 hydrogen bonds · protein-protein
E–H · 711 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6V80 · Crystal structure of human CD1d presenting alpha-Galactosylceramide in complex with NKT12… · the same entry in another collection · chain J against J, TM-score 1.00
P15813 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D (P15813) · a predicted model of the same protein · chain A 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 A0A0B4J240
Every structure of UniProt K7N5M3
Every structure of UniProt K7N5M4
Elsewhere: RCSB PDB 6V80 · PDBe 6V80 · UniProt P15813 · UniProt P61769 · UniProt A0A0B4J240 · UniProt K7N5M3 · UniProt K7N5M4

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