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Yorodumi- PDB-4oya: Human solAC Complexed with (4-Aminofurazan-3-yl)-[3-(1H-benzoimid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oya | ||||||
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Title | Human solAC Complexed with (4-Aminofurazan-3-yl)-[3-(1H-benzoimidazol-2-ylmethoxy)phenyl]methanone | ||||||
Components | Adenylate cyclase type 10 | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / positive regulation of glycogen catabolic process / : / central region of growth cone / glucose catabolic process ...negative regulation of cardiac muscle cell contraction / astrocyte end-foot / mitochondrial ATP transmembrane transport / bicarbonate binding / epithelial cilium movement involved in extracellular fluid movement / neuron projection retraction / positive regulation of glycogen catabolic process / : / central region of growth cone / glucose catabolic process / regulation of mitophagy / regulation of membrane repolarization / adenylate cyclase / basal part of cell / positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cAMP biosynthetic process / positive regulation of ossification / adenylate cyclase activity / positive regulation of protein targeting to mitochondrion / positive regulation of reactive oxygen species biosynthetic process / neuron projection extension / positive regulation of vascular associated smooth muscle cell apoptotic process / positive regulation of mitochondrial depolarization / positive regulation of ATP biosynthetic process / positive regulation of cardiac muscle hypertrophy / positive regulation of cardiac muscle cell apoptotic process / negative regulation of mitochondrial membrane potential / spermatid development / positive regulation of axon extension / Hedgehog 'off' state / negative regulation of reactive oxygen species biosynthetic process / neuron projection maintenance / positive regulation of peptidyl-threonine phosphorylation / cilium / manganese ion binding / ATPase binding / cytoskeleton / intracellular signal transduction / apical plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / magnesium ion binding / mitochondrion / extracellular region / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.03 Å | ||||||
Authors | Vinkovic, M. | ||||||
Citation | Journal: Chemmedchem / Year: 2014 Title: Crystal structure of human soluble adenylate cyclase reveals a distinct, highly flexible allosteric bicarbonate binding pocket. Authors: Saalau-Bethell, S.M. / Berdini, V. / Cleasby, A. / Congreve, M. / Coyle, J.E. / Lock, V. / Murray, C.W. / O'Brien, M.A. / Rich, S.J. / Sambrook, T. / Vinkovic, M. / Yon, J.R. / Jhoti, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oya.cif.gz | 216 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oya.ent.gz | 171 KB | Display | PDB format |
PDBx/mmJSON format | 4oya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oya_validation.pdf.gz | 754.2 KB | Display | wwPDB validaton report |
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Full document | 4oya_full_validation.pdf.gz | 761 KB | Display | |
Data in XML | 4oya_validation.xml.gz | 24.9 KB | Display | |
Data in CIF | 4oya_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/4oya ftp://data.pdbj.org/pub/pdb/validation_reports/oy/4oya | HTTPS FTP |
-Related structure data
Related structure data | 4oybC 4oyiC 4oymC 4oyoC 4oypC 4oywC 4oyxC 4oyzC 4oz2C 4oz3C 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 53466.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADCY10, SAC / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96PN6, adenylate cyclase |
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#2: Chemical | ChemComp-1VE / ( |
#3: Chemical | ChemComp-GOL / |
#4: 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: 2.63 Å3/Da / Density % sol: 53.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 1ul of protein solution was mixed with 1ul of reservoir solution (0.1M sodium acetate, pH 4.8, 0.2M trisodium citrate, 16-18% PEG4K and 10% glycerol) and left to equilibrate at 4C |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0332 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→28.77 Å / Num. obs: 35499 / % possible obs: 99.5 % / Redundancy: 2.6 % / Biso Wilson estimate: 25.15 Å2 / Net I/σ(I): 13.4 |
-Processing
Software |
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Refinement | Resolution: 2.03→28.77 Å / Cor.coef. Fo:Fc: 0.9534 / Cor.coef. Fo:Fc free: 0.9236 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.154 / SU Rfree Cruickshank DPI: 0.149
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Displacement parameters | Biso mean: 32.751 Å2
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Refine analyze | Luzzati coordinate error obs: 0.207 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.03→28.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.09 Å / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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