Research workbench
Crystal structure of xaa-pro dipeptidase from xanthomonas campestris in citrate condition
Analyse Crystal structure of xaa-pro dipeptidase from xanthomonas campestris in citrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CIK
- Type
- protein
- Length
- 794 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline dipeptidase
- EC
- 3.4.13.9
- UniProt
- Q8P839
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proline dipeptidase (EC 3.4.13.9) | protein | 397 | 36% helix, 22% strand | Q8P839 |
Ligands and binding sites
- CIT · Citric acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 586 | 0.75 | 0.82 | 61 | CIT |
| 2 | 353 | 0.67 | 0.81 | 44 | CIT |
| 3 | 344 | 0.66 | 0.80 | 38 | empty |
| 4 | 97 | 0.45 | 0.79 | 19 | empty |
| 5 | 70 | 0.34 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1740 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5CIK · Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris in citrate condition · 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 Q8P839
- Elsewhere: RCSB PDB 5CIK · PDBe 5CIK · UniProt Q8P839
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