Research workbench
The complex structure of encm with hydroxytetraketide
Analyse The complex structure of encm with hydroxytetraketide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W8Z
- Type
- protein
- Length
- 921 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative FAD-dependent oxygenase encm
- EC
- 1.13.12.-
- UniProt
- Q9KHK2
- Ligands
- FAD, HTK
- Pockets
- 6 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative FAD-dependent oxygenase encm (EC 1.13.12.-) | protein | 460 | 36% helix, 24% strand | Q9KHK2 |
| B | Putative FAD-dependent oxygenase encm (EC 1.13.12.-) | protein | 461 | 36% helix, 24% strand | Q9KHK2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- HTK · (7S)-7-hydroxy-1-phenyloctane-1,3,5-trione · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.89 | 0.91 | 104 | FAD, HTK |
| 2 | 824 | 0.89 | 0.91 | 107 | FAD, HTK |
| 3 | 388 | 0.76 | 0.86 | 52 | empty |
| 4 | 398 | 0.76 | 0.86 | 50 | empty |
| 5 | 298 | 0.60 | 0.79 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 2266 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (flavinylation).
Compared structures
- 3W8Z · The complex structure of EncM with hydroxytetraketide · 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 Q9KHK2
- Elsewhere: RCSB PDB 3W8Z · PDBe 3W8Z · UniProt Q9KHK2
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