MolNFT v1 · #115246 · protein
Proline dipeptidase from deinococcus radiodurans R1
5CDV: “Proline dipeptidase from deinococcus radiodurans R1”. X-ray diffraction, 3 ligands (MN, NA, PO4), 3 pockets (best druggability 0.43). MolNFT v1 #115246 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CDV
- Type
- protein
- Length
- 349 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline dipeptidase
- UniProt
- Q9RUY4
- Ligands
- MN, NA, PO4
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline dipeptidase | protein | 349 | 37% helix, 27% strand | Q9RUY4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.43 | 0.79 | 19 | empty |
| 2 | 94 | 0.41 | 0.78 | 22 | PO4 |
| 3 | 130 | 0.39 | 0.74 | 21 | PO4 |
Compared structures
- 5CDV · Proline dipeptidase from Deinococcus radiodurans R1 · 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 Q9RUY4
- Elsewhere: RCSB PDB 5CDV · PDBe 5CDV · UniProt Q9RUY4
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