MolNFT v1 · #61112 · protein

Structure of chicken CD1-2 with bound fatty acid

3DBX · CD1-2 antigen: “Structure of chicken CD1-2 with bound fatty acid”. X-ray diffraction, 2 ligands (PLM, NAG), 5 pockets (best druggability 0.80). MolNFT v1 #61112 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3DBX
Type: protein
Length: 378 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CD1-2 antigen; Beta-2-microglobulin
UniProt: Q5GL29, P61769
Ligands: PLM, NAG
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CD1-2 antigen	protein	279	23% helix, 41% strand	Q5GL29
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769

Ligands and binding sites

PLM · Palmitic acid · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 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	200	0.80	0.94	26	PLM
2	429	0.65	0.78	36	empty
3	81	0.40	0.78	15	empty
4	115	0.40	0.75	20	empty
5	66	0.39	0.79	16	empty

Interfaces

1 interface between chains.

A–B · 1309 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

3DBX · Structure of chicken CD1-2 with bound fatty acid · the same entry in another collection · chain A against A, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q5GL29
Every structure of UniProt P61769
Elsewhere: RCSB PDB 3DBX · PDBe 3DBX · UniProt Q5GL29 · UniProt P61769

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