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- PDB-5m78: Human Carbonic Anhydrase II in complex with fragment-like inhibitor. -
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Open data
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Basic information
Entry | Database: PDB / ID: 5m78 | ||||||
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Title | Human Carbonic Anhydrase II in complex with fragment-like inhibitor. | ||||||
![]() | Carbonic anhydrase 2 | ||||||
![]() | LYASE / PROTEIN-LIGAND-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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gloeckner, S. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II. Authors: Glockner, S. / Heine, A. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.1 KB | Display | ![]() |
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PDB format | ![]() | 144.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 735.3 KB | Display | ![]() |
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Full document | ![]() | 735.7 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rm1C ![]() 6rmpC ![]() 6s9zC ![]() 6sacC ![]() 6sasC ![]() 6sayC ![]() 6sb7C ![]() 6sdjC ![]() 3ks3S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29806.588 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The first five residues (GSPEF) are residues from an expression tag. Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 248 molecules ![](data/chem/img/DMS.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MBO.gif)
![](data/chem/img/SAL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MBO.gif)
![](data/chem/img/SAL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DMS / |
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#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-MBO / |
#5: Chemical | ChemComp-SAL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.38 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: Crystallization: 2 uL protein solution in 50 mM Tris, pH=7.8 mixed with 2 uL (NH4)2SO4, 100 mM Tris, pH=7.8, satured with PCMB and placed as hanging drop. Crystals appeared after a few days. ...Details: Crystallization: 2 uL protein solution in 50 mM Tris, pH=7.8 mixed with 2 uL (NH4)2SO4, 100 mM Tris, pH=7.8, satured with PCMB and placed as hanging drop. Crystals appeared after a few days. The crystal for data collection was soaked in 5 uL containing 35 % PEG 3350 (50 % w/v), 20 % NaCl (1 M), 25 % PEG 400, 10 % H2O, 10 % Ligandstock in DMSO (1 M) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7999 Å / Relative weight: 1 |
Reflection | Resolution: 1.077→41.423 Å / Num. obs: 103054 / % possible obs: 98.3 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rsym value: 0.066 / Net I/σ(I): 9.87 |
Reflection shell | Resolution: 1.077→1.14 Å / Redundancy: 3.64 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.36 / CC1/2: 0.846 / % possible all: 95 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KS3 Resolution: 1.077→35.631 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.077→35.631 Å
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Refine LS restraints |
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LS refinement shell |
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