MolNFT v1 · #117278 · protein
Structure of human DPP3 in complex with opioid peptide leu-enkephalin
5E3A · Dipeptidyl peptidase 3: “Structure of human DPP3 in complex with opioid peptide leu-enkephalin”. X-ray diffraction, 3 ligands (MG, ZN, K), 7 pockets (best druggability 0.85). MolNFT v1 #117278 on GenesisL1: 3D structure, binding…
- PDB
- 5E3A
- Type
- protein
- Length
- 730 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 3; Leu-enkephalin
- EC
- 3.4.14.4
- UniProt
- Q9NY33
- Ligands
- MG, ZN, K
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 3 (EC 3.4.14.4) | protein | 725 | 48% helix, 16% strand | Q9NY33 |
| B | Leu-enkephalin | protein | 5 | 0% helix, 40% 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 584 | 0.85 | 0.90 | 74 | MG |
| 2 | 73 | 0.74 | 0.98 | 24 | empty |
| 3 | 360 | 0.73 | 0.84 | 57 | empty |
| 4 | 329 | 0.69 | 0.82 | 48 | empty |
| 5 | 101 | 0.55 | 0.84 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 653 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5E3A · Structure of human DPP3 in complex with opioid peptide leu-enkephalin · 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 5E3A · PDBe 5E3A · UniProt Q9NY33
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