Research workbench
Mopii from clostridium pasteurianum complexed with molybdate
Analyse Mopii from clostridium pasteurianum complexed with molybdate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GUO
- Type
- protein
- Length
- 400 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Molybdate binding protein II
- UniProt
- P08854
- Ligands
- MOO
- Pockets
- 6 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Molybdate binding protein II | protein | 67 | 13% helix, 52% strand | P08854 |
| C, F | Molybdate binding protein II | protein | 66 | 18% helix, 52% strand | P08854 |
Ligands and binding sites
- 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 | 64 | 0.36 | 0.77 | 12 | empty |
| 2 | 58 | 0.34 | 0.77 | 11 | empty |
| 3 | 69 | 0.33 | 0.75 | 14 | empty |
| 4 | 68 | 0.33 | 0.75 | 14 | empty |
| 5 | 69 | 0.32 | 0.74 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–C · 577 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 573 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 563 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 555 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 544 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1GUO · MopII from Clostridium pasteurianum complexed with molybdate · the same entry in another collection · chain F against F, 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 C 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 P08854
- Elsewhere: RCSB PDB 1GUO · PDBe 1GUO · UniProt P08854
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