Research workbench
Crystal structure of ssopox ASC6 mutant (L72I-Y99F-I122L-L228M-F229S- W263L)
Analyse Crystal structure of ssopox ASC6 mutant (L72I-Y99F-I122L-L228M-F229S- W263L) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W3Z
- Type
- protein
- Length
- 1,205 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 · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 293 | 48% helix, 12% strand | Q97VT7 |
| B | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 302 | 47% helix, 13% strand | Q97VT7 |
| C | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 296 | 46% helix, 14% strand | Q97VT7 |
| D | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 314 | 46% helix, 12% 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 · 6 copies · chains A, C, B, D
- GOL · Glycerol · additive · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.80 | 0.85 | 59 | EDO |
| 2 | 747 | 0.77 | 0.81 | 60 | EDO |
| 3 | 567 | 0.67 | 0.77 | 54 | empty |
| 4 | 430 | 0.62 | 0.76 | 45 | empty |
| 5 | 249 | 0.59 | 0.79 | 28 | empty |
Interfaces
3 interfaces between chains.
- B–D · 1587 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1350 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 311 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5W3Z · Crystal structure of SsoPox AsC6 mutant (L72I-Y99F-I122L-L228M-F229S-W263L) · 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 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 5W3Z · PDBe 5W3Z · UniProt Q97VT7
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