Research workbench
Prolidase from pyrococcus furiosus
Analyse Prolidase from pyrococcus furiosus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PV9
- Type
- protein
- Length
- 655 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xaa-pro dipeptidase
- EC
- 3.4.13.9
- UniProt
- P81535
- Ligands
- ZN
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 337 | 37% helix, 26% strand | P81535 |
| B | Xaa-pro dipeptidase (EC 3.4.13.9) | protein | 318 | 36% helix, 25% strand | P81535 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.71 | 0.81 | 52 | empty |
| 2 | 543 | 0.69 | 0.79 | 61 | ZN |
| 3 | 303 | 0.63 | 0.80 | 34 | empty |
| 4 | 142 | 0.58 | 0.83 | 26 | empty |
| 5 | 68 | 0.33 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1796 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
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 P81535
- Elsewhere: RCSB PDB 1PV9 · PDBe 1PV9 · UniProt P81535
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.