Research workbench
Crystal structure of ssopox ASD6 mutant (V27A-Y97W-L228M-W263M) - open form
Analyse Crystal structure of ssopox ASD6 mutant (V27A-Y97W-L228M-W263M) - open form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W3W
- Type
- protein
- Length
- 1,199 residues
- Chains
- 4
- 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
- 13 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 300 | 44% helix, 11% strand | Q97VT7 |
| B | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 299 | 44% helix, 13% strand | Q97VT7 |
| C | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 298 | 46% helix, 14% strand | Q97VT7 |
| D | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 302 | 46% helix, 13% strand | Q97VT7 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, D, B, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.80 | 0.84 | 53 | EDO, GOL |
| 2 | 840 | 0.79 | 0.82 | 68 | EDO |
| 3 | 263 | 0.60 | 0.79 | 30 | empty |
| 4 | 352 | 0.59 | 0.76 | 41 | empty |
| 5 | 223 | 0.56 | 0.78 | 27 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1429 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1383 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 430 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5W3W · Crystal structure of SsoPox AsD6 mutant (V27A-Y97W-L228M-W263M) - open form · the same entry in another collection · chain C against C, 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 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 Q97VT7
- Elsewhere: RCSB PDB 5W3W · PDBe 5W3W · UniProt Q97VT7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.