[English] 日本語
![](img/lk-miru.gif)
- PDB-3m2n: Crystal structure of human carbonic anhydrase isozyme II with 4-{... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3m2n | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human carbonic anhydrase isozyme II with 4-{2-[N-(6-chloro-5-nitropyrimidin-4-yl)amino]ethyl}benzenesulfonamide | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / sulfonamide / Lyase / Metal-binding / LYASE-LYASE INHIBITOR complex | ||||||
Function / homology | ![]() positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grazulis, S. / Manakova, E. / Golovenko, D. | ||||||
![]() | ![]() Title: Design of [(2-pyrimidinylthio)acetyl]benzenesulfonamides as inhibitors of human carbonic anhydrases. Authors: Capkauskaite, E. / Zubriene, A. / Baranauskiene, L. / Tamulaitiene, G. / Manakova, E. / Kairys, V. / Grazulis, S. / Tumkevicius, S. / Matulis, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 80.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3s8xC ![]() 3s9tC ![]() 3sapC ![]() 3saxC ![]() 3sbhC ![]() 3sbiC ![]() 2nnoS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29289.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 375 molecules ![](data/chem/img/J74.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/BCN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-J74 / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-ZN / | ||||
#4: Chemical | #5: Chemical | ChemComp-BCN / | #6: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | METAL ION NATURALLY OCCURS IN CARBONIC ANHYDRASESSequence details | 126 IS SKIPPED IN THE NUMBERING. | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.22 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Na-Bicine pH 9, 2M Na-Malonate pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K PH range: 7-9 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 20, 2009 / Details: Bent, vertically focussing mirror |
Radiation | Monochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.812 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→41.24 Å / Num. all: 28936 / Num. obs: 28936 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 8.6 / Num. unique all: 4178 / Rsym value: 0.211 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2NNO Resolution: 1.65→39.78 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.867 / SU ML: 0.066 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.049 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→39.78 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
|