Research workbench
Crystal structure of the bacillus cereus enoyl-acyl carrier protein reductase with NADP+ and indole naphthyridinone (complex form)
Analyse Crystal structure of the bacillus cereus enoyl-acyl carrier protein reductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OJF
- Type
- protein
- Length
- 1,025 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl-carrier-protein] reductase (fabl) (NADPH)
- EC
- 1.3.1.9
- UniProt
- Q81GI3
- Ligands
- IMJ, NDP
- Pockets
- 15 · best druggability 0.84
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 (fabl) (NADPH) (EC 1.3.1.9) | protein | 257 | 48% helix, 15% strand | Q81GI3 |
| D, B, C | Enoyl-[acyl-carrier-protein] reductase (fabl) (NADPH) (EC 1.3.1.9) | protein | 256 | 50% helix, 15% strand | Q81GI3 |
Ligands and binding sites
- IMJ · (2E)-N-[(1,2-dimethyl-1H-indol-3-yl)methyl]-N-methyl-3-(7-oxo-5,6,7,8-tetrahydro-1,8-naphthyridin-3-yl)prop-2-enamide · ligand · 4 copies · chains A, C, D, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.84 | 0.85 | 68 | empty |
| 2 | 800 | 0.82 | 0.85 | 78 | IMJ, NDP |
| 3 | 937 | 0.82 | 0.83 | 82 | IMJ, NDP |
| 4 | 612 | 0.81 | 0.86 | 52 | IMJ, NDP |
| 5 | 726 | 0.79 | 0.83 | 66 | IMJ, NDP |
Interfaces
6 interfaces between chains.
- A–D · 1832 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1807 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 1503 Ų buried · 18 hydrogen bonds · protein-protein
- D–C · 1460 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 582 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3OJF · Crystal Structure of the Bacillus cereus Enoyl-Acyl Carrier Protein Reductase with NADP+… · the same entry in another collection · chain C against C, TM-score 1.00
- Q81GI3 · AlphaFold monomer V2.0 prediction for enoyl-[acyl-carrier-protein] reductase [NADH] fabi… · 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 Q81GI3
- Elsewhere: RCSB PDB 3OJF · PDBe 3OJF · UniProt Q81GI3
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