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Yorodumi- PDB-5m78: Human Carbonic Anhydrase II in complex with fragment-like inhibitor. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5m78 | ||||||
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Title | Human Carbonic Anhydrase II in complex with fragment-like inhibitor. | ||||||
Components | Carbonic anhydrase 2 | ||||||
Keywords | LYASE / PROTEIN-LIGAND-COMPLEX | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.077 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 | 5m78.cif.gz | 181.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m78.ent.gz | 144.8 KB | Display | PDB format |
PDBx/mmJSON format | 5m78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m78_validation.pdf.gz | 735.3 KB | Display | wwPDB validaton report |
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Full document | 5m78_full_validation.pdf.gz | 735.7 KB | Display | |
Data in XML | 5m78_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 5m78_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m7/5m78 ftp://data.pdbj.org/pub/pdb/validation_reports/m7/5m78 | 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 (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 Details: The first five residues (GSPEF) are residues from an expression tag. 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, 248 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.7999 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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