Research workbench
Crystal structure of VmoLac in P64 space group
Analyse Crystal structure of VmoLac in P64 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RDZ
- Type
- protein
- Length
- 631 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Vulcanisaeta moutnovskia
- Molecule
- Parathion hydrolase
- UniProt
- F0QXN6
- Ligands
- MYR, CO
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Parathion hydrolase | protein | 315 | 49% helix, 13% strand | F0QXN6 |
| B | Parathion hydrolase | protein | 316 | 48% helix, 13% strand | F0QXN6 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 460 | 0.85 | 0.92 | 35 | GOL |
| 2 | 157 | 0.60 | 0.83 | 23 | MYR |
| 3 | 165 | 0.60 | 0.82 | 25 | MYR |
| 4 | 220 | 0.53 | 0.77 | 29 | empty |
| 5 | 147 | 0.51 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1752 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4RDZ · Crystal structure of vmolac in P64 space group · 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 F0QXN6
- Elsewhere: RCSB PDB 4RDZ · PDBe 4RDZ · UniProt F0QXN6
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