Research workbench
R372A mutant of xaa-pro dipeptidase from xanthomonas campestris
Analyse R372A mutant of xaa-pro dipeptidase from xanthomonas campestris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CDE
- Type
- protein
- Length
- 795 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline dipeptidase
- UniProt
- Q8P839
- Ligands
- ZN, SO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline dipeptidase | protein | 398 | 36% helix, 22% strand | Q8P839 |
| B | Proline dipeptidase | protein | 397 | 36% helix, 22% strand | Q8P839 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1019 | 0.75 | 0.78 | 102 | empty |
| 2 | 490 | 0.68 | 0.79 | 60 | SO4, ZN |
| 3 | 356 | 0.67 | 0.81 | 48 | SO4, ZN |
| 4 | 73 | 0.34 | 0.75 | 16 | empty |
| 5 | 61 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1675 Ų buried · 37 hydrogen bonds · protein-protein
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 Q8P839
- Elsewhere: RCSB PDB 5CDE · PDBe 5CDE · UniProt Q8P839
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