MolNFT v1 · #123875 · protein
Crystal structure of porphyromonas endodontalis DPP11 in complex with substrate
5JY0 · ASP/GLU-specific dipeptidyl-peptidase: “Crystal structure of porphyromonas endodontalis DPP11 in complex with substrate”. X-ray diffraction, 3 pockets (best druggability 0.77). MolNFT v1 #123875 on GenesisL1: 3D structure, binding…
- PDB
- 5JY0
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASP/GLU-specific dipeptidyl-peptidase; Leu-asp-val
- EC
- 3.4.14.-
- UniProt
- F8WQK8
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 684 | 46% helix, 15% strand | F8WQK8 |
| B | Leu-asp-val | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.77 | 0.79 | 97 | TRS |
| 2 | 182 | 0.58 | 0.81 | 30 | empty |
| 3 | 170 | 0.50 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 354 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5JY0 · Crystal structure of Porphyromonas endodontalis DPP11 in complex with substrate · 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 0.97
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 5JY0 · PDBe 5JY0 · UniProt F8WQK8
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