Research workbench
Crystal structure of the alkylsulfatase atsk, a non-heme FE(II) alphaketoglutarate dependent dioxygenase in complex with iron and alphaketoglutarate
Analyse Crystal structure of the alkylsulfatase atsk, 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
- 1OII
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alkylsulfatase atsk
- UniProt
- Q9WWU5
- Ligands
- AKG, FE2
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative alkylsulfatase atsk | protein | 253 | 23% helix, 30% strand | Q9WWU5 |
| C | Putative alkylsulfatase atsk | protein | 237 | 23% helix, 30% strand | Q9WWU5 |
| D | Putative alkylsulfatase atsk | protein | 245 | 22% helix, 31% strand | Q9WWU5 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.64 | 0.81 | 34 | empty |
| 2 | 278 | 0.61 | 0.80 | 30 | empty |
| 3 | 174 | 0.58 | 0.82 | 31 | FE2, AKG |
| 4 | 179 | 0.58 | 0.81 | 30 | FE2, AKG |
| 5 | 136 | 0.54 | 0.81 | 20 | FE2, AKG |
Interfaces
3 interfaces between chains.
- A–D · 890 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 886 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 328 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1OII · Crystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) alphaketoglutarate… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9WWU5 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent sulfate ester… · a predicted model of the same protein · chain C against A, TM-score 0.99
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 Q9WWU5
- Elsewhere: RCSB PDB 1OII · PDBe 1OII · UniProt Q9WWU5
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