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

Analyse Crystal structure of S. aureus fabi in complex with NADP and 5-pentyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4BNG
Type: protein
Length: 2,034 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: 5PP, 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, C, D, E, G, H	Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)	protein	254	50% helix, 15% strand	Q7A6D8
B, F	Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)	protein	255	51% helix, 15% strand	Q7A6D8

Ligands and binding sites

5PP · 5-pentyl-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, G, C, D, E, F, H
GLU · Glutamic acid · ligand · 5 copies · chains B, G, C, E, F

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1162	0.89	0.91	109	5PP, NAP
2	1156	0.85	0.86	64	empty
3	1167	0.85	0.85	64	empty
4	514	0.83	0.89	48	5PP, NAP
5	533	0.82	0.88	51	5PP, NAP

Interfaces

15 interfaces between chains.

C–D · 1784 Å² buried · 44 hydrogen bonds · protein-protein
G–H · 1783 Å² buried · 38 hydrogen bonds · protein-protein
E–F · 1776 Å² buried · 39 hydrogen bonds · protein-protein
A–B · 1762 Å² buried · 40 hydrogen bonds · protein-protein
F–G · 1407 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

4BNG · Crystal structure of S. aureus FabI in complex with NADP and 5-pentyl- 2-phenoxyphenol · the same entry in another collection · chain H against H, 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 4BNG · PDBe 4BNG · UniProt Q7A6D8

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