Research workbench
The structure of a proline dipeptidase from streptococcus agalactiae 2603V
Analyse The structure of a proline dipeptidase from streptococcus agalactiae 2603V in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OOO
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline dipeptidase
- UniProt
- Q8E0M4
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proline dipeptidase | protein | 132 | 39% helix, 20% strand | Q8E0M4 |
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 | 114 | 0.45 | 0.78 | 18 | empty |
| 2 | 117 | 0.42 | 0.76 | 19 | empty |
| 3 | 63 | 0.36 | 0.78 | 17 | empty |
| 4 | 51 | 0.29 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 310 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3OOO · The structure of a proline dipeptidase from Streptococcus agalactiae 2603V · 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 Q8E0M4
- Elsewhere: RCSB PDB 3OOO · PDBe 3OOO · UniProt Q8E0M4
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