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Crystal structure of porphyromonas gingivalis enoyl-acp reductase II (fabk) with cofactors NADPH and FMN
Analyse Crystal structure of porphyromonas gingivalis enoyl-acp reductase II (fabk)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IQL
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-(acyl-carrier-protein) reductase II
- EC
- 1.3.1.9
- UniProt
- Q7MAW0
- Ligands
- NDP, FMN, NA
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Enoyl-(acyl-carrier-protein) reductase II (EC 1.3.1.9) | protein | 313 | 44% helix, 16% strand | Q7MAW0 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.74 | 0.81 | 71 | FMN, NDP |
| 2 | 666 | 0.74 | 0.80 | 68 | FMN, NDP |
| 3 | 427 | 0.71 | 0.82 | 39 | empty |
| 4 | 77 | 0.32 | 0.75 | 17 | empty |
| 5 | 76 | 0.31 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2292 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 4IQL · Crystal Structure of Porphyromonas gingivalis Enoyl-ACP Reductase II (FabK) with… · 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 Q7MAW0
- Elsewhere: RCSB PDB 4IQL · PDBe 4IQL · UniProt Q7MAW0
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