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Crystal structure of S. aureus fabi in complex with NADP and 2-(2-chloro-4-nitrophenoxy)-5-ethyl-4-fluorophenol

Analyse Crystal structure of S. aureus fabi in complex with NADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4D43
Type: protein
Length: 2,032 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: NAP, 9W7, GLU
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).

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

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, F, D, E, G, H
9W7 · 2-(2-chloro-4-nitrophenoxy)-5-ethyl-4-fluorophenol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
GLU · Glutamic acid · ligand · 6 copies · chains A, B, C, F, E, G
MRD · (4R)-2-methylpentane-2,4-diol · additive · 9 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1133	0.89	0.91	96	NAP, 9W7
2	1154	0.85	0.86	63	empty
3	1167	0.85	0.85	64	empty
4	505	0.82	0.88	46	NAP, 9W7
5	531	0.82	0.88	49	NAP, 9W7

Interfaces

15 interfaces between chains.

G–H · 1803 Å² buried · 38 hydrogen bonds · protein-protein
C–D · 1790 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 1787 Å² buried · 35 hydrogen bonds · protein-protein
E–F · 1779 Å² buried · 34 hydrogen bonds · protein-protein
E–H · 1378 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

4D43 · Crystal structure of S. aureus FabI in complex with NADP and 2-(2… · the same entry in another collection · chain A against A, 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 4D43 · PDBe 4D43 · UniProt Q7A6D8

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