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Crystal structure of xaa-pro dipeptidase from xanthomonas campestris, phosphate and zn bound
Analyse Crystal structure of xaa-pro dipeptidase from xanthomonas campestris, phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FCH
- Type
- protein
- Length
- 796 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline dipeptidase; Gly-gly-gly
- EC
- 3.4.13.9
- UniProt
- Q8P839
- Ligands
- ZN, PO4
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline dipeptidase (EC 3.4.13.9) | protein | 398 | 36% helix, 22% strand | Q8P839 |
| B | Proline dipeptidase (EC 3.4.13.9) | protein | 395 | 36% helix, 22% strand | Q8P839 |
| C | Gly-gly-gly | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 513 | 0.72 | 0.81 | 71 | PO4, PEG |
| 2 | 355 | 0.67 | 0.81 | 29 | GOL, PO4 |
| 3 | 335 | 0.64 | 0.80 | 47 | GOL |
| 4 | 59 | 0.38 | 0.79 | 15 | empty |
| 5 | 78 | 0.36 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1532 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 137 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 133 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5FCH · Crystal Structure of Xaa-Pro dipeptidase from Xanthomonas campestris, phosphate and Zn… · 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 5FCH · PDBe 5FCH · UniProt Q8P839
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