Research workbench
Structure of dipeptidyl-peptidase III from Corallococcus sp. strain EGB
Analyse Structure of dipeptidyl-peptidase III from Corallococcus sp. strain EGB in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZUM
- Type
- protein
- Length
- 1,070 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Corallococcus sp. EGB
- Molecule
- dipeptidyl-peptidase III
- Ligands
- ZN
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | dipeptidyl-peptidase III | protein | 533 | 55% helix, 14% strand | — |
| B | dipeptidyl-peptidase III | protein | 537 | 56% helix, 14% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.85 | 0.95 | 54 | ZN |
| 2 | 753 | 0.84 | 0.88 | 100 | empty |
| 3 | 230 | 0.83 | 0.96 | 38 | empty |
| 4 | 681 | 0.80 | 0.84 | 79 | empty |
| 5 | 282 | 0.72 | 0.86 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1450 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 5ZUM · Structure of dipeptidyl-peptidase III from corallococcus sp. strain egb · 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
- Elsewhere: RCSB PDB 5ZUM · PDBe 5ZUM
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.