MolNFT v1 · #137557 · protein
Crystal structure of ssopox ASA1 mutant (C258L-I261F-W263A)
5VSA · Aryldialkylphosphatase: “Crystal structure of ssopox ASA1 mutant (C258L-I261F-W263A)”. X-ray diffraction, 2 ligands (FE2, CO), 8 pockets (best druggability 0.85). MolNFT v1 #137557 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5VSA
- Type
- protein
- Length
- 1,243 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 0.85
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 305 | 46% helix, 13% strand | Q97VT7 |
| B, D | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 314 | 49% helix, 13% strand | Q97VT7 |
| C | Aryldialkylphosphatase (EC 3.1.8.1) | protein | 310 | 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
- GOL · Glycerol · additive · 8 copies · chains A, D, B, C
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 | 967 | 0.85 | 0.86 | 76 | GOL |
| 2 | 1091 | 0.80 | 0.81 | 93 | GOL |
| 3 | 163 | 0.60 | 0.83 | 32 | empty |
| 4 | 196 | 0.55 | 0.79 | 27 | empty |
| 5 | 138 | 0.43 | 0.75 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1750 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 1552 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 467 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
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 5VSA · PDBe 5VSA · UniProt Q97VT7
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