Research workbench
Structure of human DPP3 in complex with endomorphin-2.
Analyse Structure of human DPP3 in complex with endomorphin-2. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EHH
- Type
- protein
- Length
- 728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 3; Endomorphin-2
- EC
- 3.4.14.4
- UniProt
- Q9NY33
- Ligands
- MG, ZN, K, NH2
- Pockets
- 4 · best druggability 0.86
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 | 49% helix, 15% strand | Q9NY33 |
| B | Endomorphin-2 | protein | 4 | 0% helix, 0% 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
- NH2 · Amino group · ion · chains A, B
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 | 1153 | 0.86 | 0.87 | 120 | MG |
| 2 | 282 | 0.68 | 0.84 | 43 | empty |
| 3 | 60 | 0.43 | 0.82 | 18 | empty |
| 4 | 61 | 0.37 | 0.79 | 23 | MG |
Interfaces
1 interface between chains.
- A–B · 614 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
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 5EHH · PDBe 5EHH · UniProt Q9NY33
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