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Crystal structure of S. aureus fabi in complex with NADPH and CG400549 (small unit cell)
Analyse Crystal structure of S. aureus fabi in complex with NADPH and CG400549 (small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CV0
- Type
- protein
- Length
- 1,017 residues
- Chains
- 4
- 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
- NDP, PT6, SO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10) | protein | 254 | 47% helix, 15% strand | Q7A6D8 |
| B | Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10) | protein | 255 | 49% helix, 15% strand | Q7A6D8 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- PT6 · 1-(3-amino-2-methylbenzyl)-4-[2-(thiophen-2-yl)ethoxy]pyridin-2(1H)-one · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.85 | 0.86 | 64 | empty |
| 2 | 587 | 0.82 | 0.87 | 49 | NDP, PT6 |
| 3 | 628 | 0.82 | 0.87 | 53 | NDP, PT6 |
| 4 | 631 | 0.81 | 0.86 | 49 | NDP, PT6 |
| 5 | 735 | 0.80 | 0.84 | 57 | NDP, PT6 |
Interfaces
6 interfaces between chains.
- C–D · 1783 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 1771 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 1405 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 1372 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 648 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4CV0 · Crystal structure of S. aureus FabI in complex with NADPH and CG400549 (small unit cell) · 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 4CV0 · PDBe 4CV0 · UniProt Q7A6D8
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