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Yorodumi- PDB-5jna: Crystal structure for the complex of human carbonic anhydrase IV ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jna | |||||||||
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Title | Crystal structure for the complex of human carbonic anhydrase IV and topiramate | |||||||||
Components | Carbonic anhydrase 4 | |||||||||
Keywords | lyase/lyase inhibitor / Carbonic anhydrase / Lyase / Zinc / Inhibitor binding / lyase-lyase inhibitor complex | |||||||||
Function / homology | Function and homology information bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / brush border membrane / carbonate dehydratase activity / 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 / brush border membrane / carbonate dehydratase activity / trans-Golgi network / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / apical plasma membrane / external side of plasma membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / zinc ion binding / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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: 2018 Title: 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: 1996 Title: Crystal structure of the secretory form of membrane-assoociated human carbonic anhydrase IV at 2.8 A resolution Authors: Stams, T. / Nair, S.K. / Okuyama, T. / Waheed, A. / Sly, W.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 | 5jna.cif.gz | 470.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jna.ent.gz | 388.6 KB | Display | PDB format |
PDBx/mmJSON format | 5jna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jna_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 5jna_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 5jna_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 5jna_validation.cif.gz | 71.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/5jna ftp://data.pdbj.org/pub/pdb/validation_reports/jn/5jna | HTTPS FTP |
-Related structure data
Related structure data | 5ipzC 5jn8C 5jn9C 5jncC 5ku6C 1zncS 5jnd 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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2 |
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3 |
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4 |
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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: Cricetulus griseus (Chinese hamster) / References: UniProt: P22748, carbonic anhydrase |
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-Non-polymers , 6 types, 910 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-TOR / [( #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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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: 51.3 % |
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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 21% 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: 2→95.85 Å / Num. obs: 80516 / % possible obs: 96.8 % / Observed criterion σ(F): -0.7 / Observed criterion σ(I): -0.7 / Redundancy: 4.7 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.4 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 1ZNC Resolution: 2→95.85 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 8.534 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.158 / 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: 27.743 Å2
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Refinement step | Cycle: LAST / Resolution: 2→95.85 Å
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Refine LS restraints |
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