Research workbench
Crystal structure of the FE(II)/ALPHA-ketoglutarate dependent taurine dioxygenase from pseudomonas putida KT2440
Analyse Crystal structure of the FE(II)/ALPHA-ketoglutarate dependent taurine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V17
- Type
- protein
- Length
- 1,104 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent taurine dioxygenase
- EC
- 1.14.11.17
- UniProt
- Q88RA3
- Ligands
- AKG
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B, D | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 276 | 29% helix, 28% strand | Q88RA3 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, C, B, 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.78 | 0.86 | 52 | empty |
| 2 | 362 | 0.76 | 0.87 | 50 | empty |
| 3 | 595 | 0.75 | 0.82 | 63 | AKG |
| 4 | 565 | 0.75 | 0.82 | 56 | AKG |
| 5 | 593 | 0.74 | 0.81 | 55 | AKG |
Interfaces
6 interfaces between chains.
- C–B · 944 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 944 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 684 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 675 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 414 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3V17 · Crystal structure of the Fe(II)/alpha-ketoglutarate dependent taurine dioxygenase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q88RA3 · AlphaFold monomer V2.0 prediction for alpha-ketoglutarate-dependent taurine dioxygenase… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q88RA3
- Elsewhere: RCSB PDB 3V17 · PDBe 3V17 · UniProt Q88RA3
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