MolNFT v1 · #75612 · protein
Crystal structure of the FE(II)/ALPHA-ketoglutarate dependent taurine dioxygenase from pseudomonas putida KT2440
3PVJ · Alpha-ketoglutarate-dependent taurine dioxygenase: “Crystal structure of the FE(II)/ALPHA-ketoglutarate dependent taurine dioxygenase from pseudomonas putida…”. X-ray diffraction, 1 ligand (CL), 11 pockets (best druggability 0.82).…
- PDB
- 3PVJ
- Type
- protein
- Length
- 1,103 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
- CL
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 275 | 29% helix, 28% strand | Q88RA3 |
| B, C, D | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 276 | 29% helix, 28% strand | Q88RA3 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.82 | 0.86 | 83 | empty |
| 2 | 620 | 0.78 | 0.83 | 59 | empty |
| 3 | 576 | 0.77 | 0.83 | 62 | empty |
| 4 | 613 | 0.76 | 0.82 | 63 | empty |
| 5 | 312 | 0.72 | 0.85 | 41 | empty |
Interfaces
6 interfaces between chains.
- B–C · 929 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 886 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 683 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 678 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 448 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3PVJ · 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 B against A, TM-score 0.98
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 3PVJ · PDBe 3PVJ · UniProt Q88RA3
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