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

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

PDB: 5MY0
Type: protein
Length: 3,400 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: COA, MLC
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 18% 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	38% helix, 19% strand	P19096
B, 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	848	38% helix, 18% strand	P19096

Ligands and binding sites

COA · Coenzyme A · ligand · 2 copies · chains A, D
MLC · Malonyl-coenzyme A · ligand · chains C

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	313	0.85	0.96	57	empty
2	315	0.85	0.95	57	empty
3	421	0.77	0.86	57	empty
4	449	0.76	0.85	59	empty
5	184	0.69	0.87	30	empty

Interfaces

3 interfaces between chains.

C–D · 2723 Å² buried · 32 hydrogen bonds · protein-protein
A–B · 2702 Å² buried · 33 hydrogen bonds · protein-protein
B–C · 944 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

5MY0 · Ks-mat di-domain of mouse fas with malonyl-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 5MY0 · PDBe 5MY0 · UniProt P19096

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