Research workbench
Crystal structure of prolyl tripeptidyl aminopeptidase from porphyromonas gingivalis
Analyse Crystal structure of prolyl tripeptidyl aminopeptidase from porphyromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D5L
- Type
- protein
- Length
- 665 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidyl aminopeptidase IV, putative
- EC
- 3.4.14.-
- UniProt
- Q7MUW6
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidyl aminopeptidase IV, putative (EC 3.4.14.-) | protein | 665 | 15% helix, 37% strand | Q7MUW6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.78 | 0.81 | 90 | empty |
| 2 | 193 | 0.52 | 0.78 | 26 | empty |
| 3 | 272 | 0.51 | 0.74 | 46 | empty |
| 4 | 68 | 0.36 | 0.77 | 18 | empty |
| 5 | 67 | 0.35 | 0.76 | 20 | empty |
Compared structures
- 2D5L · Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis · the same entry in another collection · chain A against A, TM-score 1.00
- Q7MUW6 · AlphaFold monomer V2.0 prediction for prolyl tripeptidyl peptidase (Q7MUW6) · a predicted model of the same protein · chain A 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 Q7MUW6
- Elsewhere: RCSB PDB 2D5L · PDBe 2D5L · UniProt Q7MUW6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.