MolNFT v1 · #123822 · protein
Crystal structure of porphyromonas gingivalis DPP11
5JWF · ASP/GLU-specific dipeptidyl-peptidase: “Crystal structure of porphyromonas gingivalis DPP11”. X-ray diffraction, 14 pockets (best druggability 0.72). MolNFT v1 #123822 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JWF
- Type
- protein
- Length
- 1,398 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
- B2RID1
- Pockets
- 14 · best druggability 0.72
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 | 700 | 47% helix, 16% strand | B2RID1 |
| B | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 698 | 47% helix, 16% strand | B2RID1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 900 | 0.72 | 0.77 | 83 | GOL, PGO |
| 2 | 786 | 0.70 | 0.76 | 81 | empty |
| 3 | 336 | 0.54 | 0.74 | 46 | empty |
| 4 | 156 | 0.48 | 0.77 | 23 | empty |
| 5 | 52 | 0.44 | 0.84 | 13 | GOL |
Interfaces
1 interface between chains.
- A–B · 643 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5JWF · Crystal structure of Porphyromonas gingivalis DPP11 · the same entry in another collection · chain A against A, TM-score 1.00
- B2RID1 · AlphaFold monomer V2.0 prediction for ASP/GLU-specific dipeptidyl- peptidase (B2RID1) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 B2RID1
- Elsewhere: RCSB PDB 5JWF · PDBe 5JWF · UniProt B2RID1
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