+Open data
-Basic information
Entry | Database: PDB / ID: 2nnv | ||||||
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Title | Structure of inhibitor binding to Carbonic Anhydrase II | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / zinc metalloenzyme / sulfonamide | ||||||
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 / morphogenesis of an epithelium / carbonic anhydrase / regulation of intracellular pH / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Christianson, D.W. / Jude, K.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Structural Analysis of Charge Discrimination in the Binding of Inhibitors to Human Carbonic Anhydrases I and II. Authors: Srivastava, D.K. / Jude, K.M. / Banerjee, A.L. / Haldar, M. / Manokaran, S. / Kooren, J. / Mallik, S. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nnv.cif.gz | 133.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nnv.ent.gz | 101.7 KB | Display | PDB format |
PDBx/mmJSON format | 2nnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2nnv_validation.pdf.gz | 819.9 KB | Display | wwPDB validaton report |
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Full document | 2nnv_full_validation.pdf.gz | 822.4 KB | Display | |
Data in XML | 2nnv_validation.xml.gz | 15 KB | Display | |
Data in CIF | 2nnv_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/2nnv ftp://data.pdbj.org/pub/pdb/validation_reports/nn/2nnv | HTTPS FTP |
-Related structure data
Related structure data | 2nmxC 2nn1C 2nn7C 2nngC 2nnoC 2nnsC 2cbaS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 29503.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 7.7 Details: (NH4)2SO4, Tris, pH 7.7, vapor diffusion, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2005 | |||||||||||||||
Radiation |
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Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 | |||||||||||||||
Reflection | Resolution: 1.1→80 Å / Num. obs: 90979 / % possible obs: 92.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 11.4 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.139 / Net I/σ(I): 12.8 | |||||||||||||||
Reflection shell | Resolution: 1.1→1.14 Å / Redundancy: 2 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.2 / Num. unique all: 8549 / Χ2: 0.785 / % possible all: 87.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CBA Resolution: 1.1→80 Å / Num. parameters: 21825 / Num. restraintsaints: 27367 / Cross valid method: FREE R / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 0.0385. Addition of riding hydrogens reduced Free R by 0.0157.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.64 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→80 Å
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Refine LS restraints |
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