Research workbench
Proline dipeptidase from deinococcus radiodurans (selenomethionine derivative)
Analyse Proline dipeptidase from deinococcus radiodurans (selenomethionine derivative) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CDL
- 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, PO4
- Pockets
- 4 · best druggability 0.44
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline dipeptidase | protein | 349 | 38% helix, 25% strand | Q9RUY4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 87 | 0.44 | 0.80 | 19 | empty |
| 2 | 97 | 0.43 | 0.78 | 22 | PO4 |
| 3 | 134 | 0.40 | 0.75 | 21 | PO4 |
| 4 | 51 | 0.26 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 5CDL · Proline dipeptidase from Deinococcus radiodurans (selenomethionine derivative) · 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 5CDL · PDBe 5CDL · UniProt Q9RUY4
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