Research workbench
Crystal structure of ssopox ASB5 mutant (V27A-I76T-Y97W-Y99F-L130P- L226V)
Analyse Crystal structure of ssopox ASB5 mutant (V27A-I76T-Y97W-Y99F-L130P- L226V) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W3U
- Type
- protein
- Length
- 1,173 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
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 293 | 47% helix, 12% strand | Q97VT7 |
| B | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 297 | 45% helix, 11% strand | Q97VT7 |
| C | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 289 | 43% helix, 12% strand | Q97VT7 |
| D | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 294 | 44% 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
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.80 | 0.81 | 106 | FE2, CO, EDO |
| 2 | 692 | 0.78 | 0.83 | 54 | CO |
| 3 | 785 | 0.73 | 0.78 | 67 | empty |
| 4 | 55 | 0.72 | 0.98 | 17 | empty |
| 5 | 174 | 0.44 | 0.74 | 24 | CO |
Interfaces
3 interfaces between chains.
- A–B · 1413 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1393 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 220 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5W3U · Crystal structure of SsoPox AsB5 mutant (V27A-I76T-Y97W-Y99F-L130P-L226V) · the same entry in another collection · chain D against D, TM-score 1.00
- Q97VT7 · AlphaFold monomer V2.0 prediction for aryldialkylphosphatase (Q97VT7) · a predicted model of the same protein · chain B 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 Q97VT7
- Elsewhere: RCSB PDB 5W3U · PDBe 5W3U · UniProt Q97VT7
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