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Crystal structure of a putative alpha-ketoglutarate-dependent taurine dioxygenase from burkholderia xenovorans
Analyse Crystal structure of a putative 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
- 5HSX
- Type
- protein
- Length
- 549 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-ketoglutarate-dependent taurine dioxygenase
- UniProt
- Q13YM5
- Ligands
- NA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alpha-ketoglutarate-dependent taurine dioxygenase | protein | 270 | 21% helix, 30% strand | Q13YM5 |
| B | Putative alpha-ketoglutarate-dependent taurine dioxygenase | protein | 279 | 24% helix, 29% strand | Q13YM5 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.79 | 0.93 | 38 | EDO |
| 2 | 273 | 0.61 | 0.80 | 25 | EDO |
| 3 | 336 | 0.60 | 0.77 | 44 | NA, EDO |
| 4 | 103 | 0.58 | 0.86 | 25 | EDO |
| 5 | 152 | 0.52 | 0.79 | 24 | GOL |
Interfaces
1 interface between chains.
- A–B · 1128 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5HSX · Crystal Structure of a Putative Alpha-ketoglutarate-dependent Taurine Dioxygenase from… · 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 Q13YM5
- Elsewhere: RCSB PDB 5HSX · PDBe 5HSX · UniProt Q13YM5
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