Research workbench
The crystal structure of plant sulfite oxidase provides insight into sulfite oxidation in plants and animals
Analyse The crystal structure of plant sulfite oxidase provides insight into sulfite… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OGP
- Type
- protein
- Length
- 2,328 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfite oxidase
- EC
- 1.8.3.1
- UniProt
- Q9S850
- Ligands
- MTQ, CS
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Sulfite oxidase (EC 1.8.3.1) | protein | 388 | 13% helix, 32% strand | Q9S850 |
Ligands and binding sites
- MTQ · (molybdopterin-S,S)-dioxo-thio-molybdenum(vi) · ligand · 6 copies · chains A, B, C, D, E, F
- CS · Cesium ion · metal · 12 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1026 | 0.87 | 0.88 | 92 | empty |
| 2 | 1056 | 0.84 | 0.85 | 78 | GOL |
| 3 | 1076 | 0.84 | 0.85 | 77 | GOL |
| 4 | 1062 | 0.83 | 0.84 | 70 | GOL |
| 5 | 97 | 0.78 | 0.99 | 22 | MTQ |
Interfaces
6 interfaces between chains.
- A–B · 1789 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1761 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1760 Ų buried · 23 hydrogen bonds · protein-protein
- A–E · 801 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 703 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1OGP · The crystal structure of plant sulfite oxidase provides insight into sulfite oxidation in… · the same entry in another collection · chain C against C, TM-score 1.00
- Q9S850 · AlphaFold monomer V2.0 prediction for sulfite oxidase (Q9S850) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9S850
- Elsewhere: RCSB PDB 1OGP · PDBe 1OGP · UniProt Q9S850
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