Research workbench
Arginine hydroxylase vioc in complex with (3S)-oh-arg, succinate and fe after oxygen exposure using ft-ssx methods
Analyse Arginine hydroxylase vioc in complex with (3S)-oh-arg, succinate and fe after… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y12
- Type
- protein
- Length
- 330 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent L-arginine hydroxylase
- EC
- 1.14.11.41
- UniProt
- Q6WZB0
- Ligands
- ZZU, FE
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent L-arginine hydroxylase (EC 1.14.11.41) | protein | 330 | 32% helix, 23% strand | Q6WZB0 |
Ligands and binding sites
- ZZU · (2S,3S)-3-hydroxyarginine · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.74 | 0.96 | 27 | SIN, ZZU |
| 2 | 67 | 0.50 | 0.85 | 20 | empty |
| 3 | 119 | 0.42 | 0.76 | 24 | empty |
| 4 | 61 | 0.36 | 0.78 | 14 | empty |
| 5 | 69 | 0.32 | 0.75 | 15 | empty |
Compared structures
- 6Y12 · Arginine hydroxylase VioC in complex with (3S)-OH-Arg, succinate and Fe after oxygen… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6WZB0 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent L-arginine… · a predicted model of the same protein · 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 Q6WZB0
- Elsewhere: RCSB PDB 6Y12 · PDBe 6Y12 · UniProt Q6WZB0
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