MolNFT v1 · #68517 · protein
Human dipeptidyl peptidase DPP7
3JYH · Dipeptidyl-peptidase 2: “Human dipeptidyl peptidase DPP7”. X-ray diffraction, 2 ligands (NAG, BMA), 15 pockets (best druggability 0.78). MolNFT v1 #68517 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3JYH
- Type
- protein
- Length
- 1,805 residues
- Chains
- 4
- 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, BMA
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl-peptidase 2 (EC 3.4.14.2) | protein | 452 | 45% helix, 13% strand | Q9UHL4 |
| C | Dipeptidyl-peptidase 2 (EC 3.4.14.2) | protein | 451 | 43% helix, 13% strand | Q9UHL4 |
| D | Dipeptidyl-peptidase 2 (EC 3.4.14.2) | protein | 450 | 45% helix, 13% strand | Q9UHL4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.78 | 0.99 | 17 | empty |
| 2 | 71 | 0.76 | 0.99 | 16 | empty |
| 3 | 455 | 0.73 | 0.82 | 46 | empty |
| 4 | 454 | 0.72 | 0.82 | 44 | empty |
| 5 | 430 | 0.72 | 0.82 | 45 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2205 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2191 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 14 glycan (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 3JYH · PDBe 3JYH · UniProt Q9UHL4
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