Research workbench
Vioc L-arginine hydroxylase bound to FE(II), L-arginine, and a peroxysuccinate intermediate
Analyse Vioc L-arginine hydroxylase bound to FE(II), L-arginine, and a peroxysuccinate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ALO
- Type
- protein
- Length
- 337 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
- ARG, OKG, FE2
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent L-arginine hydroxylase (EC 1.14.11.41) | protein | 337 | 35% helix, 21% strand | Q6WZB0 |
Ligands and binding sites
- ARG · Arginine · ligand · chains A
- OKG · 4-peroxy-4-oxobutanoic acid · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.75 | 0.96 | 31 | ARG, OKG |
| 2 | 167 | 0.57 | 0.81 | 24 | empty |
| 3 | 50 | 0.40 | 0.83 | 16 | empty |
| 4 | 61 | 0.36 | 0.78 | 15 | empty |
| 5 | 52 | 0.29 | 0.76 | 11 | empty |
Compared structures
- 6ALO · VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and a peroxysuccinate… · 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 6ALO · PDBe 6ALO · UniProt Q6WZB0
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