Research workbench
Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate from porphyromonas gingivalis (space)
Analyse Crystal structure of dipeptidyl peptidase 11 (DPP11) with citrate from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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