MolNFT v1 · #153880 · protein
Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate from porphyromonas gingivalis (space)
6JTB · ASP/GLU-specific dipeptidyl-peptidase: “Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate from porphyromonas gingivalis (space)”. X-ray diffraction, 1 ligand (K), 6 pockets (best druggability 0.66). MolNFT v1 #153880…
- PDB
- 6JTB
- Type
- protein
- Length
- 699 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
- B2RID1
- Ligands
- K
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 699 | 50% helix, 15% strand | B2RID1 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- CIT · Citric acid · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.66 | 0.77 | 53 | PEG, CIT, GOL, K |
| 2 | 340 | 0.58 | 0.77 | 39 | PEG, CIT, K |
| 3 | 54 | 0.43 | 0.83 | 14 | GOL |
| 4 | 54 | 0.39 | 0.80 | 14 | empty |
| 5 | 111 | 0.36 | 0.73 | 21 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6JTB · Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate from Porphyromonas… · 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 A against A, TM-score 0.90
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 6JTB · PDBe 6JTB · UniProt B2RID1
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