MolNFT v1 · #138249 · protein
Phosphotriesterase variant S4
5WCW · Phosphotriesterase variant pte-R1: “Phosphotriesterase variant S4”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.67). MolNFT v1 #138249 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WCW
- Type
- protein
- Length
- 624 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase variant pte-R1
- UniProt
- A0A060GZX0
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase variant pte-R1 | protein | 311 | 52% helix, 14% strand | A0A060GZX0 |
| G | Phosphotriesterase variant pte-R1 | protein | 313 | 52% helix, 16% strand | A0A060GZX0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains A, G
- CAC · Cacodylate ion · additive · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.67 | 0.89 | 33 | empty |
| 2 | 229 | 0.52 | 0.76 | 28 | CAC |
| 3 | 168 | 0.50 | 0.77 | 19 | CAC |
| 4 | 67 | 0.34 | 0.76 | 14 | empty |
| 5 | 66 | 0.33 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–G · 1335 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 5WCW · Phosphotriesterase variant S3 · the same entry in another collection · 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 A0A060GZX0
- Elsewhere: RCSB PDB 5WCW · PDBe 5WCW · UniProt A0A060GZX0
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