MolNFT v1 · #88734 · protein

Crystal structure of S. aureus fabi in complex with NADP and 4-fluoro- 5-hexyl-2-phenoxyphenol

4D42 · Enoyl-[acyl-carrier-protein] reductase [NADPH]: “Crystal structure of S. aureus fabi in complex with NADP and 4-fluoro- 5-hexyl-2-phenoxyphenol”. X-ray diffraction, 3 ligands (W0I, NAP, GLU), 20 pockets (best druggability 0.89).…

PDB: 4D42
Type: protein
Length: 2,037 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Enoyl-[acyl-carrier-protein] reductase [NADPH]
EC: 1.3.1.10
UniProt: Q7A6D8
Ligands: W0I, NAP, GLU
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F	Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)	protein	255	49% helix, 15% strand	Q7A6D8
E, G, H	Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)	protein	254	50% helix, 15% strand	Q7A6D8

Ligands and binding sites

W0I · 4-fluoro-5-hexyl-2-phenoxyphenol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, F, D, E, G, H
GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, F, E, G

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

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1186	0.89	0.91	101	NAP, W0I
2	1109	0.85	0.86	70	empty
3	1116	0.85	0.86	65	empty
4	558	0.82	0.88	55	NAP, W0I
5	497	0.82	0.89	52	NAP, W0I

Interfaces

15 interfaces between chains.

C–D · 1813 Å² buried · 38 hydrogen bonds · protein-protein
G–H · 1808 Å² buried · 38 hydrogen bonds · protein-protein
A–B · 1794 Å² buried · 42 hydrogen bonds · protein-protein
E–F · 1790 Å² buried · 38 hydrogen bonds · protein-protein
A–D · 1426 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

4D42 · Crystal structure of S. aureus FabI in complex with NADP and 4-fluoro… · the same entry in another collection · chain C against C, TM-score 1.00

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 Q7A6D8
Elsewhere: RCSB PDB 4D42 · PDBe 4D42 · UniProt Q7A6D8

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