Research workbench
X-ray crystal structure of his-tagged Y140F FTMOX1 bound to FE(II) and 2-oxoglutarate
Analyse X-ray crystal structure of his-tagged Y140F FTMOX1 bound to FE(II) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OXH
- Type
- protein
- Length
- 574 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Verruculogen synthase
- EC
- 1.14.11.38
- UniProt
- Q4WAW9
- Ligands
- AKG, FE2
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Verruculogen synthase (EC 1.14.11.38) | protein | 285 | 27% helix, 23% strand | Q4WAW9 |
| B | Verruculogen synthase (EC 1.14.11.38) | protein | 289 | 26% helix, 22% strand | Q4WAW9 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.78 | 0.98 | 24 | empty |
| 2 | 392 | 0.75 | 0.85 | 46 | FE2, AKG |
| 3 | 354 | 0.74 | 0.85 | 45 | FE2, AKG |
| 4 | 180 | 0.52 | 0.78 | 22 | empty |
| 5 | 154 | 0.47 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2537 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 6OXH · X-ray crystal structure of His-tagged Y140F FtmOx1 bound to Fe(II) and 2-oxoglutarate · the same entry in another collection · chain A against A, TM-score 1.00
- Q4WAW9 · AlphaFold monomer V2.0 prediction for verruculogen synthase (Q4WAW9) · a predicted model of the same protein · chain A 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 Q4WAW9
- Elsewhere: RCSB PDB 6OXH · PDBe 6OXH · UniProt Q4WAW9
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