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Crystal structure of the kdo hydroxylase kdoo, a non-heme FE(II) alphaketoglutarate dependent dioxygenase in complex with COBALT(II)
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
- 5YKA
- Type
- protein
- Length
- 297 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein kdoo
- UniProt
- B3DUR4
- Ligands
- CO, SO4, CL
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein kdoo | protein | 297 | 38% helix, 20% strand | B3DUR4 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 4 copies · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- PG4 · Tetraethylene glycol · additive · 8 copies · chains A
- ACT · Acetate ion · additive · 4 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 | 679 | 0.72 | 0.78 | 62 | CO, SO4, ACT |
| 2 | 54 | 0.32 | 0.77 | 14 | PG4 |
Compared structures
- 5YKA · 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 5YKA · PDBe 5YKA · UniProt B3DUR4
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