Research workbench
Crystal structure of porphyromonas endodontalis DPP11 in complex with dipeptide arg-asp
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
- 5JWG
- Type
- protein
- Length
- 1,402 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
- NA
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 705 | 48% helix, 16% strand | F8WQK8 |
| B | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 697 | 43% helix, 16% strand | F8WQK8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.75 | 0.78 | 98 | empty |
| 2 | 870 | 0.73 | 0.78 | 75 | empty |
| 3 | 776 | 0.68 | 0.75 | 65 | empty |
| 4 | 225 | 0.64 | 0.83 | 25 | empty |
| 5 | 219 | 0.62 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 734 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5JWG · Crystal structure of Porphyromonas endodontalis DPP11 in complex with dipeptide Arg-Asp · 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 B against A, TM-score 0.99
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 5JWG · PDBe 5JWG · UniProt F8WQK8
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