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

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: 4BNH
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: NAP, 6PN, GLU
Pockets: 20 · best druggability 0.90

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, H	Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)	protein	254	51% helix, 15% strand	Q7A6D8
B, C, E, F, G	Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)	protein	255	49% helix, 15% strand	Q7A6D8

Ligands and binding sites

NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
6PN · 5-hexyl-2-phenoxyphenol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
GLU · Glutamic acid · ligand · 7 copies · chains A, E, B, C, F, 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	1149	0.90	0.91	109	NAP, 6PN
2	1093	0.85	0.86	65	empty
3	1115	0.85	0.86	66	empty
4	607	0.83	0.88	65	NAP, 6PN
5	530	0.82	0.88	50	NAP, 6PN

Interfaces

15 interfaces between chains.

C–D · 1815 Å² buried · 44 hydrogen bonds · protein-protein
G–H · 1804 Å² buried · 43 hydrogen bonds · protein-protein
E–F · 1786 Å² buried · 37 hydrogen bonds · protein-protein
A–B · 1783 Å² buried · 40 hydrogen bonds · protein-protein
B–C · 1416 Å² buried · 28 hydrogen bonds · protein-protein

Compared structures

4BNH · Crystal structure of S. aureus FabI in complex with NADP and 5-hexyl- 2-phenoxyphenol · 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 4BNH · PDBe 4BNH · UniProt Q7A6D8

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