MolNFT v1 · #17103 · protein
Crystal structure of the alkylsulfatase atsk, a non-heme FE(II) alphaketoglutarate dependent dioxygenase in complex with alphaketoglutarate
1OIJ · Putative alkylsulfatase atsk: “Crystal structure of the alkylsulfatase atsk, a non-heme FE(II) alphaketoglutarate dependent dioxygenase in…”. X-ray diffraction, 2 ligands (AKG, NA), 12 pockets (best druggability 0.61). MolNFT v1…
- PDB
- 1OIJ
- Type
- protein
- Length
- 983 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alkylsulfatase atsk
- UniProt
- Q9WWU5
- Ligands
- AKG, NA
- Pockets
- 12 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alkylsulfatase atsk | protein | 254 | 22% helix, 30% strand | Q9WWU5 |
| B | Putative alkylsulfatase atsk | protein | 255 | 22% helix, 30% strand | Q9WWU5 |
| C | Putative alkylsulfatase atsk | protein | 238 | 23% helix, 30% strand | Q9WWU5 |
| D | Putative alkylsulfatase atsk | protein | 236 | 23% helix, 31% strand | Q9WWU5 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- NA · Sodium 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
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 272 | 0.61 | 0.80 | 30 | empty |
| 2 | 267 | 0.60 | 0.79 | 30 | empty |
| 3 | 172 | 0.58 | 0.81 | 25 | NA, AKG |
| 4 | 127 | 0.55 | 0.82 | 23 | NA, AKG |
| 5 | 189 | 0.46 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–D · 887 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 884 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 337 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1OIJ · 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 1OIJ · PDBe 1OIJ · UniProt Q9WWU5
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