Research workbench
Crystal structure of a new dpp III family member
Analyse Crystal structure of a new dpp III family member in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YFB
- Type
- protein
- Length
- 1,381 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase 3
- EC
- 3.4.14.4
- UniProt
- B0S4Q0
- Ligands
- ZN
- Pockets
- 12 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase 3 (EC 3.4.14.4) | protein | 691 | 49% helix, 18% strand | B0S4Q0 |
| B | Dipeptidyl peptidase 3 (EC 3.4.14.4) | protein | 690 | 49% helix, 18% strand | B0S4Q0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.90 | 0.92 | 133 | GOL |
| 2 | 1155 | 0.90 | 0.91 | 121 | EDO |
| 3 | 142 | 0.54 | 0.81 | 24 | EDO |
| 4 | 133 | 0.51 | 0.80 | 23 | empty |
| 5 | 79 | 0.40 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 260 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5YFB · Crystal structure of a new DPP III family member · the same entry in another collection · 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 B0S4Q0
- Elsewhere: RCSB PDB 5YFB · PDBe 5YFB · UniProt B0S4Q0
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