Research workbench
Crystal structure of S. aureus fabi in complex with NADPH and kalimantacin B
Analyse Crystal structure of S. aureus fabi in complex with NADPH and kalimantacin B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TBC
- Type
- protein
- Length
- 2,070 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl-carrier-protein] reductase [NADPH]
- EC
- 1.3.1.39
- UniProt
- A0A0J9X1X7
- Ligands
- NDP, N5H
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.39) | protein | 260 | 49% helix, 15% strand | A0A0J9X1X7 |
| C, G | Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.39) | protein | 259 | 48% helix, 15% strand | A0A0J9X1X7 |
| D, E, F, H | Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.39) | protein | 258 | 48% helix, 15% strand | A0A0J9X1X7 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- N5H · (2~{E},5~{R},10~{E},12~{E},15~{S},19~{R})-20-[[(2~{R}, 3~{R})-3-aminocarbonyloxy-2-methyl-butanoyl]amino]-3, 5,15-trimethyl-7-methylidene-19-oxidanyl-17-oxidanylidene-icosa-2,10,12-trienoic acid · ligand · 8 copies · chains A, B, C, D, E, F, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.85 | 0.86 | 63 | empty |
| 2 | 1146 | 0.85 | 0.86 | 63 | empty |
| 3 | 615 | 0.84 | 0.89 | 50 | NDP, N5H |
| 4 | 560 | 0.83 | 0.88 | 48 | NDP, N5H |
| 5 | 667 | 0.83 | 0.87 | 51 | NDP, N5H |
Interfaces
16 interfaces between chains.
- C–D · 1800 Ų buried · 41 hydrogen bonds · protein-protein
- G–H · 1797 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 1789 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 1785 Ų buried · 41 hydrogen bonds · protein-protein
- A–D · 1779 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6TBC · Crystal structure of S. aureus FabI in complex with NADPH and kalimantacin B · 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 A0A0J9X1X7
- Elsewhere: RCSB PDB 6TBC · PDBe 6TBC · UniProt A0A0J9X1X7
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