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E. COLI fabh with small molecule inhibitor 1

Analyse E. COLI fabh with small molecule inhibitor 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BNM
Type: protein
Length: 634 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-oxoacyl-[acyl-carrier-protein] synthase 3
EC: 2.3.1.180
UniProt: P0A6R0
Ligands: 4VK, SO4
Pockets: 6 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180)	protein	317	40% helix, 27% strand	P0A6R0

Ligands and binding sites

4VK · N-{[3'-(hydroxymethyl)biphenyl-4-yl]methyl}benzenesulfonamide · ligand · chains A
SO4 · Sulfate ion · ion · chains A
PG4 · Tetraethylene glycol · additive · chains B

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	250	0.77	0.90	53	empty
2	186	0.61	0.82	33	4VK
3	132	0.59	0.84	27	PG4
4	109	0.39	0.75	19	empty
5	98	0.35	0.74	25	empty

Interfaces

1 interface between chains.

A–B · 2262 Å² buried · 49 hydrogen bonds · protein-protein

Compared structures

5BNM · E. coli FabH with Small Molecule Inhibitor 1 · the same entry in another collection · chain A against A, TM-score 1.00
P0A6R0 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 3… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P0A6R0
Elsewhere: RCSB PDB 5BNM · PDBe 5BNM · UniProt P0A6R0

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