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Yorodumi- PDB-4x3v: Crystal structure of human ribonucleotide reductase 1 bound to in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x3v | |||||||||
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Title | Crystal structure of human ribonucleotide reductase 1 bound to inhibitor | |||||||||
Components | Ribonucleoside-diphosphate reductase large subunit | |||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Complex / reducatse / inhibitor / enzyme / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / 2'-deoxyribonucleotide biosynthetic process / mitochondrial DNA replication / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor ...ribonucleoside-diphosphate reductase activity / pyrimidine nucleobase metabolic process / cell proliferation in forebrain / ribonucleoside diphosphate metabolic process / positive regulation of G0 to G1 transition / 2'-deoxyribonucleotide biosynthetic process / mitochondrial DNA replication / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / Interconversion of nucleotide di- and triphosphates / deoxyribonucleotide biosynthetic process / protein heterotetramerization / response to ionizing radiation / DNA synthesis involved in DNA repair / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / cell projection / male gonad development / disordered domain specific binding / retina development in camera-type eye / nuclear envelope / DNA repair / neuronal cell body / mitochondrion / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | |||||||||
Authors | Dealwis, C.G. / Ahmad, M.F. / Alam, I. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Med.Chem. / Year: 2015 Title: Identification of Non-nucleoside Human Ribonucleotide Reductase Modulators. Authors: Ahmad, M.F. / Huff, S.E. / Pink, J. / Alam, I. / Zhang, A. / Perry, K. / Harris, M.E. / Misko, T. / Porwal, S.K. / Oleinick, N.L. / Miyagi, M. / Viswanathan, R. / Dealwis, C.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x3v.cif.gz | 295.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x3v.ent.gz | 233.4 KB | Display | PDB format |
PDBx/mmJSON format | 4x3v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x3v_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4x3v_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4x3v_validation.xml.gz | 59.6 KB | Display | |
Data in CIF | 4x3v_validation.cif.gz | 78.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x3/4x3v ftp://data.pdbj.org/pub/pdb/validation_reports/x3/4x3v | HTTPS FTP |
-Related structure data
Related structure data | 3hncS 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: 90179.023 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RRM1, RR1 / Production host: Escherichia coli (E. coli) References: UniProt: P23921, ribonucleoside-diphosphate reductase #2: Chemical | #3: Chemical | ChemComp-3X4 / | |
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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: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.9 Details: 0.1 M Tris-HCl pH 7.9, 0.2 M LiSO4, 19% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→200 Å / Num. obs: 19866 / % possible obs: 95.6 % / Redundancy: 3.2 % / Net I/σ(I): 32.6 |
Reflection shell | Resolution: 3.9→4.04 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 4.5 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HNC Resolution: 3.7→108.361 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.7→108.361 Å
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Refine LS restraints |
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LS refinement shell |
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