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Ks-mat di-domain of mouse fas with octanoyl CoA

Analyse Ks-mat di-domain of mouse fas with octanoyl CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ROP
Type: protein
Length: 3,382 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fatty acid synthase
EC: 2.3.1.85, 2.3.1.38, 2.3.1.39, 2.3.1.41, 1.1.1.100, 4.2.1.59, 1.3.1.39, 3.1.2.14
UniProt: P19096
Ligands: OCA, CO8
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Fatty acid synthase (EC 2.3.1.85, 2.3.1.38, 2.3.1.39, 2.3.1.41, 1.1.1.100, 4.2.1.59, 1.3.1.39, 3.1.2.14)	protein	852	37% helix, 18% strand	P19096
B	Fatty acid synthase (EC 2.3.1.85, 2.3.1.38, 2.3.1.39, 2.3.1.41, 1.1.1.100, 4.2.1.59, 1.3.1.39, 3.1.2.14)	protein	831	35% helix, 17% strand	P19096
C	Fatty acid synthase (EC 2.3.1.85, 2.3.1.38, 2.3.1.39, 2.3.1.41, 1.1.1.100, 4.2.1.59, 1.3.1.39, 3.1.2.14)	protein	847	35% helix, 18% strand	P19096

Ligands and binding sites

OCA · Octanoic acid (caprylic acid) · ligand · 5 copies · chains A, B, C, D
CO8 · Octanoyl-coenzyme A · ligand · chains D

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	882	0.87	0.89	127	OCA
2	1076	0.86	0.87	157	OCA
3	1060	0.81	0.82	109	empty
4	1039	0.78	0.80	106	empty
5	317	0.77	0.88	48	OCA, CO8

Interfaces

3 interfaces between chains.

C–D · 2685 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 2685 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 930 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 covalent (covalent ligand).

Compared structures

6ROP · Ks-mat di-domain of mouse fas with octanoyl CoA · the same entry in another collection · chain D against D, TM-score 1.00
P19096 · AlphaFold monomer V2.0 prediction for fatty acid synthase (P19096) · a predicted model of the same protein · chain A 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 P19096
Elsewhere: RCSB PDB 6ROP · PDBe 6ROP · UniProt P19096

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