+
Open data
-
Basic information
Entry | Database: PDB / ID: 6r9u | ||||||
---|---|---|---|---|---|---|---|
Title | Human Cyclophilin D in complex with fragment | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | ||||||
![]() | ISOMERASE / CYCLOPHILIN / BETA BARREL / PROLYL CIS/TRANS ISOMERASE / MITOC | ||||||
Function / homology | ![]() regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation ...regulation of proton-transporting ATPase activity, rotational mechanism / negative regulation of oxidative phosphorylation uncoupler activity / mitochondrial outer membrane permeabilization involved in programmed cell death / regulation of mitochondrial membrane permeability involved in programmed necrotic cell death / skeletal muscle fiber differentiation / mitochondrial permeability transition pore complex / mitochondrial depolarization / cellular response to arsenic-containing substance / negative regulation of ATP-dependent activity / negative regulation of oxidative phosphorylation / regulation of mitochondrial membrane permeability / cyclosporin A binding / negative regulation of release of cytochrome c from mitochondria / apoptotic mitochondrial changes / necroptotic process / protein peptidyl-prolyl isomerization / negative regulation of intrinsic apoptotic signaling pathway / cellular response to calcium ion / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to ischemia / cellular response to hydrogen peroxide / protein folding / mitochondrial inner membrane / mitochondrial matrix / negative regulation of apoptotic process / mitochondrion / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Graedler, U. | ||||||
![]() | ![]() Title: Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies. Authors: Gradler, U. / Schwarz, D. / Blaesse, M. / Leuthner, B. / Johnson, T.L. / Bernard, F. / Jiang, X. / Marx, A. / Gilardone, M. / Lemoine, H. / Roche, D. / Jorand-Lebrun, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 91.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 782.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 782.8 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r8lC ![]() 6r8oC ![]() 6r8wC ![]() 6r9sC ![]() 6r9xC ![]() 6ra1C ![]() 4j5bS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 17652.125 Da / Num. of mol.: 1 / Fragment: 44-207 (K175I) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 219 molecules ![](data/chem/img/JVQ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-JVQ / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-SO4 / | ||||
#4: Chemical | #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.32 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 50 mM potassium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→51.02 Å / Num. obs: 51798 / % possible obs: 100 % / Redundancy: 15.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 23.09 |
Reflection shell | Resolution: 1.26→1.51 Å / Redundancy: 15 % / Rmerge(I) obs: 0.578 / Num. unique obs: 21350 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4J5B Resolution: 1.26→51.02 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→51.02 Å
|