Research workbench
Crystal structure of the lactonase LMO2620 from listeria monocytogenes
Analyse Crystal structure of the lactonase LMO2620 from listeria monocytogenes in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PNZ
- Type
- protein
- Length
- 1,970 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphotriesterase family protein
- UniProt
- Q4EFN5
- Ligands
- ZN, PO4
- Pockets
- 19 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphotriesterase family protein | protein | 329 | 51% helix, 15% strand | Q4EFN5 |
| C, D, E, F | Phosphotriesterase family protein | protein | 328 | 52% helix, 16% strand | Q4EFN5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 21 copies · chains A, B, C, D, E, F
- GOL · Glycerol · additive · 21 copies · chains A, E, B, C, F, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.67 | 0.83 | 31 | empty |
| 2 | 285 | 0.67 | 0.82 | 34 | empty |
| 3 | 265 | 0.66 | 0.82 | 36 | empty |
| 4 | 251 | 0.66 | 0.83 | 34 | empty |
| 5 | 691 | 0.66 | 0.74 | 66 | empty |
Interfaces
7 interfaces between chains.
- B–D · 633 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 633 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 630 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 628 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (carboxylation).
Compared structures
- 3PNZ · Crystal structure of the lactonase Lmo2620 from Listeria monocytogenes · 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 Q4EFN5
- Elsewhere: RCSB PDB 3PNZ · PDBe 3PNZ · UniProt Q4EFN5
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