MolNFT v1 · #146218 · protein
X-ray crystal structure of vioc bound to vanadyl ion, L-homoarginine, and succinate
6DB2 · Alpha-ketoglutarate-dependent L-arginine hydroxylase: “X-ray crystal structure of vioc bound to vanadyl ion, L-homoarginine, and succinate”. X-ray diffraction, 2 ligands (HRG, VVO), 4 pockets (best druggability 0.67). MolNFT v1…
- PDB
- 6DB2
- Type
- protein
- Length
- 336 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
- HRG, VVO
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent L-arginine hydroxylase (EC 1.14.11.41) | protein | 336 | 33% helix, 23% strand | Q6WZB0 |
Ligands and binding sites
- HRG · L-homoarginine · ligand · chains A
- VVO · oxovanadium(2+) · ligand · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- SIN · Succinic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.67 | 0.89 | 37 | HRG, VVO |
| 2 | 158 | 0.56 | 0.81 | 24 | empty |
| 3 | 56 | 0.35 | 0.78 | 14 | empty |
| 4 | 64 | 0.31 | 0.75 | 15 | empty |
Compared structures
- 6DB2 · X-ray crystal structure of VioC bound to vanadyl ion, L-homoarginine, 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 6DB2 · PDBe 6DB2 · UniProt Q6WZB0
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