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The crystal structure of the molybdenum storage protein from azotobacter vinelandii loaded with polyoxotungstates (wsto)
Analyse The crystal structure of the molybdenum storage protein from azotobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OGX
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdenum storage protein subunit alpha; Molybdenum storage protein subunit beta
- UniProt
- P84308, P84253
- Ligands
- WO3, ATP, W, MG, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Molybdenum storage protein subunit alpha | protein | 246 | 43% helix, 17% strand | P84308 |
| B | Molybdenum storage protein subunit beta | protein | 268 | 43% helix, 15% strand | P84253 |
Ligands and binding sites
- WO3 · Tri-tungsten(vi) oxide complex · ligand · chains A
- ATP · Adenosine-5'-triphosphate · ligand · chains A, B
- W · Tungsten ion · metal · 23 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- PO4 · Phosphate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.77 | 0.91 | 38 | MG, ATP |
| 2 | 294 | 0.69 | 0.83 | 33 | PO4 |
| 3 | 165 | 0.46 | 0.75 | 25 | W |
| 4 | 153 | 0.41 | 0.74 | 25 | empty |
| 5 | 70 | 0.36 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2279 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 2OGX · The crystal structure of the molybdenum storage protein from Azotobacter vinelandii… · the same entry in another collection · chain A against A, TM-score 1.00
- P84308 · AlphaFold monomer V2.0 prediction for molybdenum storage protein subunit alpha (P84308) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P84253 · AlphaFold monomer V2.0 prediction for molybdenum storage protein subunit beta (P84253) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P84308
- Every structure of UniProt P84253
- Elsewhere: RCSB PDB 2OGX · PDBe 2OGX · UniProt P84308 · UniProt P84253
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