Research workbench
Crystal structure of fabi from S. aureus in complex with a novel benzimidazole inhibitor
Analyse Crystal structure of fabi from S. aureus in complex with a novel benzimidazole… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NZ9
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl-carrier-protein] reductase [NADPH]
- EC
- 1.3.1.39
- UniProt
- Q2FI66
- Ligands
- 1JT, NAP
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.39) | protein | 255 | 49% helix, 15% strand | Q2FI66 |
| B | Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.39) | protein | 254 | 49% helix, 15% strand | Q2FI66 |
Ligands and binding sites
- 1JT · 1-(4-methoxy-3-methylbenzyl)-5,6,7,8-tetrahydro-1H-naphtho[2,3-d]imidazole · ligand · 2 copies · chains A, B
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.82 | 0.85 | 60 | 1JT, NAP |
| 2 | 771 | 0.81 | 0.84 | 66 | 1JT, NAP |
| 3 | 273 | 0.57 | 0.77 | 36 | empty |
| 4 | 220 | 0.51 | 0.76 | 27 | empty |
| 5 | 75 | 0.40 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1390 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4NZ9 · Crystal Structure of FabI from S. aureus in complex with a novel benzimidazole inhibitor · 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 Q2FI66
- Elsewhere: RCSB PDB 4NZ9 · PDBe 4NZ9 · UniProt Q2FI66
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