Research workbench
Structure of human DPP3 in complex with hemorphin like opioid peptide ivypw
Analyse Structure of human DPP3 in complex with hemorphin like opioid peptide ivypw in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5E3C
- Type
- protein
- Length
- 729 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 3; Ivypw
- EC
- 3.4.14.4
- UniProt
- Q9NY33
- Ligands
- MG, ZN, K
- Pockets
- 4 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 3 (EC 3.4.14.4) | protein | 724 | 48% helix, 15% strand | Q9NY33 |
| B | Ivypw | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A, B
- K · Potassium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1164 | 0.87 | 0.88 | 132 | MG |
| 2 | 400 | 0.75 | 0.85 | 55 | empty |
| 3 | 75 | 0.46 | 0.82 | 21 | empty |
| 4 | 62 | 0.41 | 0.81 | 21 | MG |
Interfaces
1 interface between chains.
- A–B · 726 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5E3C · Structure of human DPP3 in complex with hemorphin like opioid peptide IVYPW · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NY33 · AlphaFold monomer V2.0 prediction for dipeptidyl peptidase 3 (Q9NY33) · a predicted model of the same protein · 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 Q9NY33
- Elsewhere: RCSB PDB 5E3C · PDBe 5E3C · UniProt Q9NY33
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.