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Yorodumi- PDB-5ku6: Crystal structure for the complex of human carbonic anhydrase IV ... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5ku6 | |||||||||
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| Title | Crystal structure for the complex of human carbonic anhydrase IV and methazolamide | |||||||||
Components | Carbonic anhydrase 4 | |||||||||
Keywords | lyase/lyase inhibitor / Carbonic anhydrase / Intrinsic thermodynamics / lyase / inhibitor / lyase-lyase inhibitor complex | |||||||||
| Function / homology | Function and homology informationbicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / brush border membrane / trans-Golgi network ...bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / brush border membrane / trans-Golgi network / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / apical plasma membrane / external side of plasma membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / extracellular exosome / zinc ion binding / membrane / plasma membrane Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Chen, Z. / Waheed, A. / Di Cera, E. / Sly, W.S. | |||||||||
| Funding support | United States, 2items
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Citation | Journal: Eur. Biophys. J. / Year: 2018Title: Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV. Authors: Mickeviciute, A. / Timm, D.D. / Gedgaudas, M. / Linkuviene, V. / Chen, Z. / Waheed, A. / Michailoviene, V. / Zubriene, A. / Smirnov, A. / Capkauskaite, E. / Baranauskiene, L. / Jachno, J. / ...Authors: Mickeviciute, A. / Timm, D.D. / Gedgaudas, M. / Linkuviene, V. / Chen, Z. / Waheed, A. / Michailoviene, V. / Zubriene, A. / Smirnov, A. / Capkauskaite, E. / Baranauskiene, L. / Jachno, J. / Revuckiene, J. / Manakova, E. / Grazulis, S. / Matuliene, J. / Di Cera, E. / Sly, W.S. / Matulis, D. #1: Journal: PNAS / Year: 1996Title: Crystal structure of the secretory form of membrane-associated human carbonic anhydrase IV at 2.8 A resolution Authors: Stams, T. / Nair, S.K. / Okuyama, T. / Waheed, A. / Sly, W.S. / Christianson, W. | |||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5ku6.cif.gz | 468.4 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5ku6.ent.gz | 387.3 KB | Display | PDB format |
| PDBx/mmJSON format | 5ku6.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/5ku6 ftp://data.pdbj.org/pub/pdb/validation_reports/ku/5ku6 | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 5ipzC ![]() 5jn8C ![]() 5jn9C ![]() 5jnaC ![]() 5jncC ![]() 1zncS 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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| 1 | ![]()
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| 2 | ![]()
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| 3 | ![]()
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| 4 | ![]()
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| 5 |
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| Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
| #1: Protein | Mass: 30364.473 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CA4 / Production host: ![]() |
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-Non-polymers , 6 types, 939 molecules 










| #2: Chemical | ChemComp-MZM / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
| Has protein modification | 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: 2.5 Å3/Da / Density % sol: 50.87 % |
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| Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 100 mM Na acetate, 200 mM AmSO4 and 23% PEG 4000 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
| Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 26, 2015 |
| Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
| Reflection | Resolution: 1.8→40 Å / Num. obs: 110310 / % possible obs: 97.3 % / Observed criterion σ(F): -0.5 / Observed criterion σ(I): -0.5 / Redundancy: 4.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.4 |
| Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.1 / % possible all: 94.2 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 1ZNC Resolution: 1.8→95.78 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.494 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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| 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: 22.503 Å2
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| Refinement step | Cycle: LAST / Resolution: 1.8→95.78 Å
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| Refine LS restraints |
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About Yorodumi



Homo sapiens (human)
X-RAY DIFFRACTION
United States, 2items
Citation















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