MolNFT v1 · #138554 · protein
Phosphotriesterase variant S7
5WMS: “Phosphotriesterase variant S7”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.66). MolNFT v1 #138554 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WMS
- Type
- protein
- Length
- 1,260 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase
- UniProt
- A0A060GYS1
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphotriesterase | protein | 315 | 52% helix, 16% strand | A0A060GYS1 |
| G | Phosphotriesterase | protein | 315 | 52% helix, 17% strand | A0A060GYS1 |
| Q | Phosphotriesterase | protein | 316 | 53% helix, 15% strand | A0A060GYS1 |
| S | Phosphotriesterase | protein | 314 | 52% helix, 15% strand | A0A060GYS1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, G, Q, S
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 9 copies · chains A, G, Q, S
- CAC · Cacodylate ion · additive · 4 copies · chains A, G, Q, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.66 | 0.86 | 37 | empty |
| 2 | 165 | 0.64 | 0.86 | 34 | empty |
| 3 | 351 | 0.58 | 0.76 | 31 | CAC, MPD |
| 4 | 265 | 0.55 | 0.77 | 27 | ZN, CAC |
| 5 | 248 | 0.54 | 0.77 | 27 | CAC, MPD |
Interfaces
3 interfaces between chains.
- Q–S · 1359 Ų buried · 37 hydrogen bonds · protein-protein
- A–G · 1328 Ų buried · 34 hydrogen bonds · protein-protein
- A–Q · 206 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5WMS · Phosphotriesterase variant S7 · 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 A0A060GYS1
- Elsewhere: RCSB PDB 5WMS · PDBe 5WMS · UniProt A0A060GYS1
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