Research workbench
Crystal structure of putative nitroalkan dioxygenase (TM0800) from thermotoga maritima at 2.71 a resolution
Analyse Crystal structure of putative nitroalkan dioxygenase (TM0800) from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BO9
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative nitroalkan dioxygenase
- EC
- 1.3.1.9
- UniProt
- Q9WZQ7
- Ligands
- SO4, PO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative nitroalkan dioxygenase (EC 1.3.1.9) | protein | 314 | 45% helix, 16% strand | Q9WZQ7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- 2PE · Nonaethylene glycol · additive · 9 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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.74 | 0.82 | 66 | PO4, SO4 |
| 2 | 505 | 0.74 | 0.82 | 66 | PO4, SO4 |
| 3 | 649 | 0.68 | 0.77 | 35 | 2PE |
| 4 | 78 | 0.38 | 0.78 | 21 | 2PE |
| 5 | 76 | 0.38 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2230 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3BO9 · Crystal structure of putative nitroalkan dioxygenase (TM0800) from Thermotoga maritima at… · 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 Q9WZQ7
- Elsewhere: RCSB PDB 3BO9 · PDBe 3BO9 · UniProt Q9WZQ7
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