Research workbench
Mopii from clostridium pasteurianum complexed with molybdate (partial)
Analyse Mopii from clostridium pasteurianum complexed with molybdate (partial) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GUN
- Type
- protein
- Length
- 402 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdate binding protein II
- UniProt
- P08854
- Ligands
- CA, MOO
- Pockets
- 6 · best druggability 0.38
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Molybdate binding protein II | protein | 67 | 19% helix, 52% strand | P08854 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B, D, E, F
- MOO · Molybdate ion · ion · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 90 | 0.38 | 0.76 | 18 | empty |
| 2 | 59 | 0.36 | 0.78 | 13 | empty |
| 3 | 70 | 0.36 | 0.76 | 12 | empty |
| 4 | 66 | 0.36 | 0.77 | 12 | empty |
| 5 | 68 | 0.36 | 0.77 | 11 | empty |
Interfaces
6 interfaces between chains.
- D–F · 574 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 567 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 566 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 559 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 559 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1GUN · MopII from Clostridium pasteurianum complexed with molybdate (partial) · the same entry in another collection · chain D against D, TM-score 1.00
- P08854 · AlphaFold monomer V2.0 prediction for molybdenum-pterin-binding protein 2 (P08854) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P08854
- Elsewhere: RCSB PDB 1GUN · PDBe 1GUN · UniProt P08854
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