Research workbench
Crystal structure of porphyromonas gingivalis dipeptidyl peptidase 4
Analyse Crystal structure of porphyromonas gingivalis dipeptidyl peptidase 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OLJ
- Type
- protein
- Length
- 703 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl peptidase IV
- UniProt
- B2RKU3
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl peptidase IV | protein | 703 | 16% helix, 37% strand | B2RKU3 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.71 | 0.77 | 76 | GOL |
| 2 | 268 | 0.64 | 0.81 | 36 | empty |
| 3 | 501 | 0.57 | 0.73 | 52 | empty |
| 4 | 105 | 0.39 | 0.75 | 15 | empty |
| 5 | 52 | 0.30 | 0.77 | 10 | empty |
Compared structures
- 5OLJ · Crystal structure of Porphyromonas gingivalis dipeptidyl peptidase 4 · 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 B2RKU3
- Elsewhere: RCSB PDB 5OLJ · PDBe 5OLJ · UniProt B2RKU3
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