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Crystal structure of the kdo hydroxylase kdoo, a non-heme FE(II) alphaketoglutarate dependent dioxygenase in complex with alphaketoglutarate and FE(III)
Analyse Crystal structure of the kdo hydroxylase kdoo, a non-heme FE(II)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YVZ
- Type
- protein
- Length
- 294 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein kdoo
- UniProt
- B3DUR4
- Ligands
- AKG, FE, SO4
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein kdoo | protein | 294 | 37% helix, 20% strand | B3DUR4 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · chains A
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · 4 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.62 | 0.77 | 47 | AKG, PG4 |
| 2 | 59 | 0.30 | 0.75 | 12 | empty |
Compared structures
- 5YVZ · Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate… · the same entry in another collection · 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 B3DUR4
- Elsewhere: RCSB PDB 5YVZ · PDBe 5YVZ · UniProt B3DUR4
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