MolNFT v1 · #26053 · protein

Fatty acid beta-oxidation multienzyme complex from pseudomonas fragi, form I (NATIVE2)

1WDK · Fatty oxidation complex alpha subunit: “Fatty acid beta-oxidation multienzyme complex from pseudomonas fragi, form I (NATIVE2)”. X-ray diffraction, 5 ligands (N8E, NAD, ACO), 20 pockets (best druggability 0.80). MolNFT v1 #26053 on…

PDB: 1WDK
Type: protein
Length: 2,199 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fatty oxidation complex alpha subunit; 3-ketoacyl-CoA thiolase
EC: 4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3, 2.3.1.16
UniProt: P28793, P28790
Ligands: N8E, NAD, ACO, HG, ZN
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 53% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fatty oxidation complex alpha subunit (EC 4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3)	protein	708	56% helix, 12% strand	P28793
B	Fatty oxidation complex alpha subunit (EC 4.2.1.17, 5.3.3.8, 1.1.1.35, 5.1.2.3)	protein	711	56% helix, 12% strand	P28793
C, D	3-ketoacyl-CoA thiolase (EC 2.3.1.16)	protein	390	40% helix, 23% strand	P28790

Ligands and binding sites

N8E · 3,6,9,12,15-pentaoxatricosan-1-ol · ligand · 4 copies · chains A, B
NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
ACO · Acetyl coenzyme *A · ligand · 2 copies · chains C, D
HG · Mercury (II) ion · metal · 2 copies · chains C, D
ZN · Zinc ion · metal · chains A

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	972	0.80	0.81	95	empty
2	729	0.76	0.81	53	empty
3	742	0.75	0.80	90	NAD, N8E
4	58	0.72	0.98	18	empty
5	367	0.71	0.83	43	N8E

Interfaces

6 interfaces between chains.

C–D · 2731 Å² buried · 67 hydrogen bonds · protein-protein
A–B · 840 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 837 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 783 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 524 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

1WDK · fatty acid beta-oxidation multienzyme complex from Pseudomonas fragi, form I (native2) · the same entry in another collection · chain A against A, TM-score 1.00
P28790 · AlphaFold monomer V2.0 prediction for 3-ketoacyl-CoA thiolase (P28790) · a predicted model of the same protein · chain D against A, TM-score 1.00
P28793 · AlphaFold monomer V2.0 prediction for fatty acid oxidation complex subunit alpha (P28793) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P28793
Every structure of UniProt P28790
Elsewhere: RCSB PDB 1WDK · PDBe 1WDK · UniProt P28793 · UniProt P28790

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