MolNFT v1 · #124425 · protein
Crystal structure of a taurine dioxygenase from burkholderia xenovorans
5KEU: “Crystal structure of a taurine dioxygenase from burkholderia xenovorans”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.78). MolNFT v1 #124425 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KEU
- Type
- protein
- Length
- 551 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Taurine dioxygenase
- UniProt
- Q13IQ2
- Ligands
- MG
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Taurine dioxygenase | protein | 271 | 24% helix, 32% strand | Q13IQ2 |
| B | Taurine dioxygenase | protein | 280 | 25% helix, 28% strand | Q13IQ2 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- FMT · Formic acid · additive · 23 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.78 | 0.97 | 20 | FMT |
| 2 | 340 | 0.65 | 0.80 | 24 | FMT |
| 3 | 150 | 0.55 | 0.81 | 28 | FMT |
| 4 | 192 | 0.53 | 0.78 | 26 | EDO |
| 5 | 141 | 0.52 | 0.80 | 28 | FMT |
Interfaces
1 interface between chains.
- A–B · 1310 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5KEU · Crystal Structure of a Taurine Dioxygenase from Burkholderia xenovorans · 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 Q13IQ2
- Elsewhere: RCSB PDB 5KEU · PDBe 5KEU · UniProt Q13IQ2
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