Research workbench
Crystal structure of ssopox ASA6 mutant (F46L-C258A-W263M-I280T) - open form
Analyse Crystal structure of ssopox ASA6 mutant (F46L-C258A-W263M-I280T) - open form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VRK
- Type
- protein
- Length
- 628 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aryldialkylphosphatase
- EC
- 3.1.8.1
- UniProt
- Q97VT7
- Ligands
- FE2, CO
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 314 | 45% helix, 14% strand | Q97VT7 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 428 | 0.83 | 0.90 | 31 | empty |
| 2 | 330 | 0.65 | 0.80 | 44 | GOL, EDO |
| 3 | 304 | 0.65 | 0.81 | 37 | EDO |
| 4 | 237 | 0.47 | 0.74 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1746 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 5VRK · Crystal structure of SsoPox AsA6 mutant (F46L-C258A-W263M-I280T) - open form · the same entry in another collection · chain A against A, TM-score 1.00
- Q97VT7 · AlphaFold monomer V2.0 prediction for aryldialkylphosphatase (Q97VT7) · 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 Q97VT7
- Elsewhere: RCSB PDB 5VRK · PDBe 5VRK · UniProt Q97VT7
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