MolNFT v1 · #154557 · protein

OSACBP2 in complex with C18:3-CoA

6KF8 · Acyl-CoA-binding domain-containing protein 2: “OSACBP2 in complex with C18:3-CoA”. X-ray diffraction, 7 pockets (best druggability 0.77). MolNFT v1 #154557 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6KF8
Type: protein
Length: 534 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Acyl-CoA-binding domain-containing protein 2
UniProt: Q5VRM0
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Acyl-CoA-binding domain-containing protein 2	protein	87	70% helix, 0% strand	Q5VRM0
A, D, F	Acyl-CoA-binding domain-containing protein 2	protein	89	71% helix, 0% strand	Q5VRM0
I, K	Acyl-CoA-binding domain-containing protein 2	protein	90	69% helix, 0% strand	Q5VRM0

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1123	0.77	0.79	110	empty
2	413	0.66	0.79	59	empty
3	347	0.55	0.74	34	empty
4	145	0.50	0.78	17	empty
5	151	0.43	0.75	17	empty

Interfaces

11 interfaces between chains.

C–F · 437 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 333 Å² buried · 3 hydrogen bonds · protein-protein
F–I · 224 Å² buried · 2 hydrogen bonds · protein-protein
A–F · 219 Å² buried · 4 hydrogen bonds · protein-protein
D–K · 191 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6KF8 · OsACBP2 in complex with C18:3-CoA · the same entry in another collection · chain K against K, TM-score 1.00
Q5VRM0 · AlphaFold monomer V2.0 prediction for acyl-CoA-binding domain- containing protein 2… · a predicted model of the same protein · chain D 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 Q5VRM0
Elsewhere: RCSB PDB 6KF8 · PDBe 6KF8 · UniProt Q5VRM0

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