Research workbench
Crystal structure of a phosphotriesterase-like lactonase gkap in native form
Analyse Crystal structure of a phosphotriesterase-like lactonase gkap in native form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WVX
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase
- EC
- 3.5.-.-
- UniProt
- Q5KZU5
- Ligands
- CO
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphotriesterase (EC 3.5.-.-) | protein | 323 | 46% helix, 15% strand | Q5KZU5 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.67 | 0.85 | 32 | EDO |
| 2 | 321 | 0.66 | 0.81 | 64 | EDO |
| 3 | 363 | 0.62 | 0.78 | 53 | empty |
| 4 | 82 | 0.38 | 0.77 | 14 | empty |
| 5 | 67 | 0.37 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1673 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (carboxylation).
Compared structures
- 4WVX · Crystal structure of a phosphotriesterase-like lactonase Gkap in native form · 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 Q5KZU5
- Elsewhere: RCSB PDB 4WVX · PDBe 4WVX · UniProt Q5KZU5
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