MolNFT v1 · #105473 · protein
Crystal structure of xaa-pro dipeptidase from xanthomonas campestris
4R60 · Proline dipeptidase: “Crystal structure of xaa-pro dipeptidase from xanthomonas campestris”. X-ray diffraction, 3 ligands (MN, NA, PO4), 5 pockets (best druggability 0.72). MolNFT v1 #105473 on GenesisL1: 3D structure, binding sites…
- PDB
- 4R60
- Type
- protein
- Length
- 795 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
- Ligands
- MN, NA, PO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline dipeptidase (EC 3.4.13.9) | protein | 397 | 36% helix, 22% strand | Q8P839 |
| B | Proline dipeptidase (EC 3.4.13.9) | protein | 398 | 36% helix, 22% strand | Q8P839 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 389 | 0.72 | 0.83 | 54 | MN |
| 2 | 324 | 0.71 | 0.84 | 44 | empty |
| 3 | 361 | 0.66 | 0.80 | 48 | empty |
| 4 | 291 | 0.63 | 0.80 | 43 | empty |
| 5 | 65 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1630 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 4R60 · Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris · 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 4R60 · PDBe 4R60 · UniProt Q8P839
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