MolNFT v1 · #115100 · protein

Human CD1C with ligands in a' and F' channel

5C9J · T-cell surface glycoprotein CD1C,T-cell surface…: “Human CD1C with ligands in a' and F' channel”. X-ray diffraction, 3 ligands (DAO, STE, PO4), 5 pockets (best druggability 0.84). MolNFT v1 #115100 on GenesisL1: 3D structure…

PDB: 5C9J
Type: protein
Length: 380 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell surface glycoprotein CD1C,T-cell surface glycoprotein CD1B; Beta-2-microglobulin
UniProt: P29017, P29016, P61769
Ligands: DAO, STE, PO4
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	T-cell surface glycoprotein CD1C,T-cell surface glycoprotein CD1B	protein	281	26% helix, 41% strand	P29017, P29016
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769

Ligands and binding sites

DAO · Lauric acid · ligand · 2 copies · chains A
STE · Stearic acid · ligand · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	664	0.84	0.87	60	DAO, STE
2	506	0.70	0.80	54	GOL, PO4
3	188	0.49	0.76	35	GOL, PO4
4	135	0.47	0.78	27	empty
5	58	0.27	0.73	11	empty

Interfaces

1 interface between chains.

A–B · 1344 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.98
P29017 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1C (P29017) · a predicted model of the same protein · chain A against A, TM-score 0.97
P29016 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD1B (P29016) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 P29017
Every structure of UniProt P29016
Every structure of UniProt P61769
Elsewhere: RCSB PDB 5C9J · PDBe 5C9J · UniProt P29017 · UniProt P29016 · UniProt P61769

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