Research workbench
Structure of the PRO-PRO endopeptidase (PPEP-2) from Paenibacillus alvei
Analyse Structure of the PRO-PRO endopeptidase (PPEP-2) from Paenibacillus alvei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FPC
- Type
- protein
- Length
- 728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.75
- Source
- Paenibacillus alvei
- Molecule
- PRO-PRO endopeptidase
- UniProt
- K4ZRC1
- Ligands
- CD, ZN, SO4
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.75 · 4 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PRO-PRO endopeptidase | protein | 185 | 55% helix, 8% strand | K4ZRC1 |
| B | PRO-PRO endopeptidase | protein | 186 | 55% helix, 9% strand | K4ZRC1 |
| C | PRO-PRO endopeptidase | protein | 188 | 53% helix, 8% strand | K4ZRC1 |
| D | PRO-PRO endopeptidase | protein | 169 | 58% helix, 9% strand | K4ZRC1 |
Ligands and binding sites
- CD · Cadmium ion · metal · 14 copies · chains A, D, B, C
- ZN · Zinc ion · metal · 4 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 14 copies · chains B, C, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 763 | 0.83 | 0.86 | 130 | SO4 |
| 2 | 458 | 0.83 | 0.90 | 63 | empty |
| 3 | 390 | 0.63 | 0.78 | 38 | SO4 |
| 4 | 103 | 0.61 | 0.87 | 21 | empty |
| 5 | 194 | 0.57 | 0.80 | 32 | SO4 |
Interfaces
6 interfaces between chains.
- B–C · 1187 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1071 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 645 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 621 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 528 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6FPC · Structure of the pro-pro endopeptidase (ppep-2) from paenibacillus alvei · the same entry in another collection · chain D against D, TM-score 1.00
- K4ZRC1 · AlphaFold monomer V2.0 prediction for pro-pro endopeptidase (K4ZRC1) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 K4ZRC1
- Elsewhere: RCSB PDB 6FPC · PDBe 6FPC · UniProt K4ZRC1
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