Research workbench
Crystal structure of S. aureus fabi in complex with NADP and 5-ethyl-4-fluoro-2-((2-fluoropyridin-3-YL)OXY)PHENOL
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
- 4D44
- 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, 1.3.1.39
- UniProt
- Q7A6D8
- Ligands
- NAP, JA3, GLU
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 51% 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, 1.3.1.39) | protein | 254 | 51% helix, 15% strand | Q7A6D8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, E, B, C, D, F, G, H
- JA3 · 5-ethyl-4-fluoro-2-[(2-fluoropyridin-3-yl)oxy]phenol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- GLU · Glutamic acid · ligand · 6 copies · chains B, C, A, E, F, G
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 8 copies · chains A, B, C, E, F, D, 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, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1196 | 0.89 | 0.90 | 95 | NAP, JA3 |
| 2 | 1150 | 0.85 | 0.86 | 64 | empty |
| 3 | 1141 | 0.85 | 0.86 | 65 | empty |
| 4 | 507 | 0.83 | 0.90 | 47 | JA3, NAP |
| 5 | 494 | 0.83 | 0.89 | 46 | JA3, NAP |
Interfaces
15 interfaces between chains.
- C–D · 1802 Ų buried · 40 hydrogen bonds · protein-protein
- G–H · 1801 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1793 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 1778 Ų buried · 40 hydrogen bonds · protein-protein
- E–H · 1374 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4D44 · Crystal structure of S. aureus FabI in complex with NADP and 5-ethyl… · 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 4D44 · PDBe 4D44 · UniProt Q7A6D8
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