Research workbench
X-ray crystal structure of vioc bound to FE(II), 3S-hydroxy-L- homoarginine, and succinate
Analyse X-ray crystal structure of vioc bound to FE(II), 3S-hydroxy-L- homoarginine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DAZ
- 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
- G3M, FE2
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent L-arginine hydroxylase (EC 1.14.11.41) | protein | 336 | 34% helix, 22% strand | Q6WZB0 |
Ligands and binding sites
- G3M · (3S)-N~6~-carbamimidoyl-3-hydroxy-L-lysine · ligand · chains A
- FE2 · Fe (II) 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
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 | 94 | 0.74 | 0.96 | 28 | FE2, SIN, G3M |
| 2 | 169 | 0.56 | 0.81 | 24 | empty |
| 3 | 66 | 0.48 | 0.84 | 19 | empty |
| 4 | 53 | 0.32 | 0.76 | 13 | empty |
| 5 | 73 | 0.31 | 0.74 | 15 | empty |
Compared structures
- 6DAZ · X-ray crystal structure of VioC bound to Fe(II), 3S-hydroxy-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 6DAZ · PDBe 6DAZ · UniProt Q6WZB0
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