Research workbench
Crystal structure of porphyromonas endodontalis DPP11 in complex with dipeptide arg-glu
Analyse Crystal structure of porphyromonas endodontalis DPP11 in complex with dipeptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JWI
- Type
- protein
- Length
- 1,378 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASP/GLU-specific dipeptidyl-peptidase
- EC
- 3.4.14.-
- UniProt
- F8WQK8
- Ligands
- CL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 699 | 50% helix, 16% strand | F8WQK8 |
| B | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 679 | 43% helix, 16% strand | F8WQK8 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.79 | 0.84 | 73 | empty |
| 2 | 918 | 0.77 | 0.80 | 102 | empty |
| 3 | 986 | 0.75 | 0.78 | 118 | empty |
| 4 | 673 | 0.66 | 0.75 | 67 | empty |
| 5 | 190 | 0.63 | 0.84 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5JWI · Crystal structure of Porphyromonas endodontalis DPP11 in complex with dipeptide Arg-Glu · the same entry in another collection · chain A against A, TM-score 1.00
- F8WQK8 · AlphaFold monomer V2.0 prediction for ASP/GLU-specific dipeptidyl- peptidase (F8WQK8) · a predicted model of the same protein · 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 F8WQK8
- Elsewhere: RCSB PDB 5JWI · PDBe 5JWI · UniProt F8WQK8
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