Research workbench
Crystal structure of vioc in complex with FE(II), (2S,3S)- hydroxyarginine, and succinate
Analyse Crystal structure of vioc in complex with FE(II), (2S,3S)- hydroxyarginine, and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WBP
- Type
- protein
- Length
- 332 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arginine beta-hydroxylase
- UniProt
- Q6WZB0
- Ligands
- ARG, ZZU, FE2
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-arginine beta-hydroxylase | protein | 332 | 33% helix, 23% strand | Q6WZB0 |
Ligands and binding sites
- ARG · Arginine · ligand · chains A
- ZZU · (2S,3S)-3-hydroxyarginine · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
- SIN · Succinic acid · additive · chains A
- GOL · Glycerol · additive · 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 | 88 | 0.74 | 0.97 | 26 | ZZU, SIN |
| 2 | 73 | 0.51 | 0.85 | 20 | empty |
| 3 | 154 | 0.49 | 0.77 | 22 | empty |
| 4 | 81 | 0.33 | 0.74 | 17 | empty |
| 5 | 55 | 0.33 | 0.77 | 16 | empty |
Compared structures
- 2WBP · Crystal structure of VioC in complex with Fe(II), (2S,3S)- hydroxyarginine, and succinate · 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 2WBP · PDBe 2WBP · UniProt Q6WZB0
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