MolNFT v1 · #90170 · protein
Structure of DPP2
4EBB · Dipeptidyl peptidase 2: “Structure of DPP2”. X-ray diffraction, 2 ligands (NAG, ZN), 6 pockets (best druggability 0.76). MolNFT v1 #90170 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4EBB
- Type
- protein
- Length
- 899 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 2
- EC
- 3.4.14.2
- UniProt
- Q9UHL4
- Ligands
- NAG, ZN
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 2 (EC 3.4.14.2) | protein | 450 | 44% helix, 13% strand | Q9UHL4 |
| B | Dipeptidyl peptidase 2 (EC 3.4.14.2) | protein | 449 | 44% helix, 13% strand | Q9UHL4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.76 | 0.83 | 52 | empty |
| 2 | 507 | 0.74 | 0.82 | 48 | empty |
| 3 | 173 | 0.55 | 0.80 | 21 | empty |
| 4 | 111 | 0.42 | 0.76 | 18 | empty |
| 5 | 103 | 0.38 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 23 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 8 disulfide, 3 glycan (engineered, disulfide, N-glycosylation).
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 Q9UHL4
- Elsewhere: RCSB PDB 4EBB · PDBe 4EBB · UniProt Q9UHL4
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