Research workbench
Crystal structure of a putative oxygenase (SO_2589) from shewanella oneidensis at 2.20 a resolution
Analyse Crystal structure of a putative oxygenase (SO_2589) from shewanella oneidensis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ON7
- Type
- protein
- Length
- 1,091 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, IRON/ASCORBATE family
- UniProt
- Q8EE01
- Ligands
- CL
- Pockets
- 12 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase, IRON/ASCORBATE family | protein | 269 | 32% helix, 22% strand | Q8EE01 |
| B | Oxidoreductase, IRON/ASCORBATE family | protein | 279 | 31% helix, 23% strand | Q8EE01 |
| C | Oxidoreductase, IRON/ASCORBATE family | protein | 270 | 31% helix, 22% strand | Q8EE01 |
| D | Oxidoreductase, IRON/ASCORBATE family | protein | 273 | 32% helix, 22% strand | Q8EE01 |
Ligands and binding sites
- CL · Chloride ion · ion · 7 copies · chains A, D, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.89 | 0.91 | 103 | empty |
| 2 | 1010 | 0.88 | 0.89 | 121 | CL |
| 3 | 1051 | 0.88 | 0.89 | 124 | CL, GOL |
| 4 | 166 | 0.70 | 0.89 | 27 | GOL |
| 5 | 264 | 0.52 | 0.75 | 44 | CL |
Interfaces
6 interfaces between chains.
- B–C · 1812 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1728 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 691 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 685 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 342 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 modified (engineered).
Compared structures
- 3ON7 · Crystal structure of a Putative oxygenase (SO_2589) from Shewanella oneidensis at 2.20 A… · 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 Q8EE01
- Elsewhere: RCSB PDB 3ON7 · PDBe 3ON7 · UniProt Q8EE01
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