Research workbench
Unique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover mechanism of reaction
Analyse Unique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V4F
- Type
- protein
- Length
- 334 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-hydroxylase
- UniProt
- C4NCJ7
- Ligands
- 5KC, FE, CO2
- Pockets
- 2 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Beta-hydroxylase | protein | 167 | 14% helix, 35% strand | C4NCJ7 |
Ligands and binding sites
- 5KC · (2S,3S)-2-azanyl-4-(2-hydroxy-2-oxoethylamino)-3-oxidanyl-butanoic acid · ligand · chains B
- FE · Fe (III) ion · metal · 4 copies · chains B, A
- CO2 · Carbon dioxide · ion · chains B
- SIN · Succinic acid · additive · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 722 | 0.76 | 0.81 | 63 | SIN, FE |
| 2 | 277 | 0.67 | 0.83 | 29 | 5KC, SIN, CO2, FE |
Interfaces
1 interface between chains.
- B–A · 448 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7V4F · Unique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover… · the same entry in another collection · chain B against B, 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 C4NCJ7
- Elsewhere: RCSB PDB 7V4F · PDBe 7V4F · UniProt C4NCJ7
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