MolNFT v1 · #140581 · protein
Crystal structure of a new dpp III family member
5YFC · Dipeptidyl peptidase 3: “Crystal structure of a new dpp III family member”. X-ray diffraction, 2 ligands (SO4, CL), 9 pockets (best druggability 0.90). MolNFT v1 #140581 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YFC
- Type
- protein
- Length
- 1,380 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
- SO4, CL
- Pockets
- 9 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Dipeptidyl peptidase 3 (EC 3.4.14.4) | protein | 690 | 50% helix, 18% strand | B0S4Q0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.90 | 0.92 | 141 | SO4, CL, TRS |
| 2 | 1133 | 0.90 | 0.92 | 141 | SO4, CL, TRS |
| 3 | 75 | 0.60 | 0.89 | 23 | empty |
| 4 | 88 | 0.55 | 0.85 | 23 | empty |
| 5 | 63 | 0.34 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 562 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5YFC · 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 5YFC · PDBe 5YFC · UniProt B0S4Q0
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