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Yorodumi- PDB-6sdj: Human Carbonic Anhydrase II in complex with (R)-1-aminopropan-2-ol -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sdj | |||||||||
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Title | Human Carbonic Anhydrase II in complex with (R)-1-aminopropan-2-ol | |||||||||
Components | Carbonic anhydrase 2 | |||||||||
Keywords | LYASE / Inhibitor / complex / CO2 conversion | |||||||||
Function / homology | Function and homology information 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 / regulation of intracellular pH / morphogenesis of an epithelium / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å | |||||||||
Authors | Gloeckner, S. / Heine, A. / Klebe, G. | |||||||||
Citation | Journal: Biomolecules / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sdj.cif.gz | 224.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sdj.ent.gz | 151.3 KB | Display | PDB format |
PDBx/mmJSON format | 6sdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sd/6sdj ftp://data.pdbj.org/pub/pdb/validation_reports/sd/6sdj | HTTPS FTP |
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-Related structure data
Related structure data | 5m78C 6rm1C 6rmpC 6s9zC 6sacC 6sasC 6sayC 6sb7C 3ks3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plus / References: UniProt: P00918, carbonic anhydrase |
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-Non-polymers , 5 types, 185 molecules
#2: Chemical | ChemComp-ZN / | ||||
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#3: Chemical | ChemComp-J3K / ( | ||||
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Ammonium sulfate 2.7 M, TRIS 0.1, saturated with para-Chloromercuribenzoic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→41.103 Å / Num. obs: 120252 / % possible obs: 98.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.64 Å2 / CC1/2: 0.998 / Rsym value: 0.048 / Net I/σ(I): 13.51 |
Reflection shell | Resolution: 1.02→1.08 Å / Mean I/σ(I) obs: 3.74 / Num. unique obs: 18157 / CC1/2: 0.96 / Rsym value: 0.175 / % possible all: 92.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3KS3 Resolution: 1.02→35.44 Å / SU ML: 0.0518 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 10.537
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.52 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.02→35.44 Å
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Refine LS restraints |
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LS refinement shell |
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