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Crystal structure of an alpha-ketoglutarate-dependent taurine dioxygenase from mycobacterium smegmatis
Analyse Crystal structure of an alpha-ketoglutarate-dependent taurine dioxygenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J5I
- Type
- protein
- Length
- 2,056 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-ketoglutarate-dependent taurine dioxygenase
- EC
- 1.14.11.17
- UniProt
- A0QZ23
- Ligands
- FE, MG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 23% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 248 | 24% helix, 30% strand | A0QZ23 |
| B | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 285 | 24% helix, 28% strand | A0QZ23 |
| C | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 271 | 22% helix, 29% strand | A0QZ23 |
| D | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 239 | 25% helix, 31% strand | A0QZ23 |
| E | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 250 | 24% helix, 30% strand | A0QZ23 |
| F | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 250 | 24% helix, 30% strand | A0QZ23 |
| G | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 264 | 22% helix, 30% strand | A0QZ23 |
| H | Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) | protein | 249 | 24% helix, 30% strand | A0QZ23 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · chains F
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.81 | 0.83 | 86 | empty |
| 2 | 1108 | 0.79 | 0.81 | 91 | EDO |
| 3 | 253 | 0.70 | 0.85 | 39 | FE |
| 4 | 346 | 0.63 | 0.79 | 43 | empty |
| 5 | 306 | 0.62 | 0.79 | 49 | empty |
Interfaces
11 interfaces between chains.
- E–G · 964 Ų buried · 20 hydrogen bonds · protein-protein
- F–H · 964 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 921 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 915 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 699 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4J5I · Crystal structure of an 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 A0QZ23
- Elsewhere: RCSB PDB 4J5I · PDBe 4J5I · UniProt A0QZ23
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