Research workbench
Crystal structure of porphyromonas endodontalis DPP11 in alternate conformation
Analyse Crystal structure of porphyromonas endodontalis DPP11 in alternate conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JXP
- Type
- protein
- Length
- 662 residues
- Chains
- 1
- 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
- CA, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 662 | 44% helix, 17% strand | F8WQK8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.78 | 0.80 | 116 | empty |
| 2 | 298 | 0.62 | 0.79 | 42 | empty |
| 3 | 63 | 0.27 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5JXP · Crystal structure of Porphyromonas endodontalis DPP11 in alternate conformation · 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 0.92
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 5JXP · PDBe 5JXP · UniProt F8WQK8
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