[English] 日本語
![](img/lk-miru.gif)
- PDB-7tgu: Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7tgu | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B1 | |||||||||||||||||||||
![]() | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | |||||||||||||||||||||
![]() | ISOMERASE/ISOMERASE inhibitor / Peptidyl-prolyl isomerase / oxidative stress / necrosis / mitochondrial permeability / ISOMERASE / ISOMERASE-ISOMERASE inhibitor complex | |||||||||||||||||||||
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 / necroptotic process / apoptotic mitochondrial changes / protein peptidyl-prolyl isomerization / negative regulation of intrinsic apoptotic signaling pathway / cellular response to calcium ion / peptide binding / 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 | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Rangwala, A.M. / Thakur, M.K. / Seeliger, M.A. / Peterson, A.A. / Liu, D.R. | |||||||||||||||||||||
Funding support | ![]()
| |||||||||||||||||||||
![]() | ![]() Title: Discovery and molecular basis of subtype-selective cyclophilin inhibitors. Authors: Peterson, A.A. / Rangwala, A.M. / Thakur, M.K. / Ward, P.S. / Hung, C. / Outhwaite, I.R. / Chan, A.I. / Usanov, D.L. / Mootha, V.K. / Seeliger, M.A. / Liu, D.R. | |||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 135.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7tgsC ![]() 7tgtC ![]() 7tgvC ![]() 7th1C ![]() 7th6C ![]() 7th7C ![]() 7thcC ![]() 7thdC ![]() 7thfC ![]() 2bitS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17666.150 Da / Num. of mol.: 1 / Mutation: K175I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-I44 / ( |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.4 % / Description: Blades and tabular, between 0.3-0.5 mm |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 23% PEG 3350 0.5 M KH2PO4 Protein and inhibitor were mixed in ratio 1:3 1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2019 |
Radiation | Monochromator: Double Crystal Monochromator; Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→44.534 Å / Num. obs: 43493 / % possible obs: 87.8 % / Redundancy: 10.8 % / Biso Wilson estimate: 11.42 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.015 / Rrim(I) all: 0.053 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.21→1.232 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 799 / CC1/2: 0.766 / CC star: 0.951 / Rpim(I) all: 0.317 / Rrim(I) all: 0.538 / % possible all: 33.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2BIT Resolution: 1.21→44.53 Å / SU ML: 0.0933 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.1107 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.21→44.53 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|