MolNFT v1 · #107873 · protein
Phosphonate monoester hydrolase sppmh from silicibacter pomeroyi
4UPK: “Phosphonate monoester hydrolase sppmh from silicibacter pomeroyi”. X-ray diffraction, 18 pockets (best druggability 0.76). MolNFT v1 #107873 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4UPK
- Type
- protein
- Length
- 1,518 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphonate monoester hydrolase
- UniProt
- Q5LKJ1
- Pockets
- 18 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Phosphonate monoester hydrolase | protein | 506 | 34% helix, 16% strand | Q5LKJ1 |
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1113 | 0.76 | 0.79 | 110 | empty |
| 2 | 502 | 0.64 | 0.76 | 45 | empty |
| 3 | 118 | 0.61 | 0.86 | 20 | empty |
| 4 | 287 | 0.59 | 0.78 | 39 | empty |
| 5 | 335 | 0.59 | 0.76 | 42 | empty |
Interfaces
2 interfaces between chains.
- A–B · 749 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 408 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4UPK · Phosphonate monoester hydrolase SpPMH from Silicibacter pomeroyi · 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 Q5LKJ1
- Elsewhere: RCSB PDB 4UPK · PDBe 4UPK · UniProt Q5LKJ1
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