+
Open data
-
Basic information
Entry | Database: PDB / ID: 6rne | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | DPP1 in complex with inhibitor | |||||||||
![]() | (Dipeptidyl peptidase ...) x 3 | |||||||||
![]() | HYDROLASE / DIPEPTIDYL PEPTIDASE I / INHIBITOR COMPLEX / Cathepsin C | |||||||||
Function / homology | ![]() dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / : / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kack, H. | |||||||||
![]() | ![]() Title: DPP1 Inhibitors: Exploring the Role of Water in the S2 Pocket of DPP1 with Substituted Pyrrolidines. Authors: Kack, H. / Doyle, K. / Hughes, S.J. / Bodnarchuk, M.S. / Lonn, H. / Van De Poel, A. / Palmer, N. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 159.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 124.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6rn6C ![]() 6rn7C ![]() 6rn9C ![]() 6rniC ![]() 1k3bS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Dipeptidyl peptidase ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 13500.163 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 18630.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Protein | Mass: 7583.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
---|---|
#5: Sugar |
-Non-polymers , 6 types, 236 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/KA8.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/KA8.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-DMS / #7: Chemical | ChemComp-KA8 / ( | #8: Chemical | ChemComp-CL / | #9: Chemical | #10: Chemical | ChemComp-PEG / | #11: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.59 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 3350, 0.2 M Ammonium sulphate, 0.1 M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN A200 / Detector: CCD / Date: Oct 9, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→28.3 Å / Num. obs: 53715 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 1.65→1.73 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.481 / Num. unique obs: 7719 / % possible all: 99.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1K3B Resolution: 1.65→28.28 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.082 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.084 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.081
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.11 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→28.28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|