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Yorodumi- PDB-2oci: Crystal structure of valacyclovir hydrolase complexed with a prod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oci | ||||||
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Title | Crystal structure of valacyclovir hydrolase complexed with a product analogue | ||||||
Components | Valacyclovir hydrolase | ||||||
Keywords | HYDROLASE / alpha beta hydrolase fold | ||||||
Function / homology | Function and homology information alpha-amino-acid esterase activity / Phase I - Functionalization of compounds / amino acid metabolic process / xenobiotic metabolic process / response to toxic substance / mitochondrial outer membrane / Hydrolases; Acting on ester bonds / mitochondrion Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Lai, L. / Xu, Z. / Amidon, G.L. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Molecular basis of prodrug activation by human valacyclovirase, an alpha-amino acid ester hydrolase. Authors: Lai, L. / Xu, Z. / Zhou, J. / Lee, K.D. / Amidon, G.L. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT OF THE PROTEIN IS NOT KNOWN |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oci.cif.gz | 72 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oci.ent.gz | 51.4 KB | Display | PDB format |
PDBx/mmJSON format | 2oci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oci_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 2oci_full_validation.pdf.gz | 426.5 KB | Display | |
Data in XML | 2oci_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 2oci_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oc/2oci ftp://data.pdbj.org/pub/pdb/validation_reports/oc/2oci | HTTPS FTP |
-Related structure data
Related structure data | 2ocgSC 2ockC 2oclC 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 on special symmetry positions |
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Details | The biological assembly of this molecule is not certain. |
-Components
#1: Protein | Mass: 28871.080 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BPHL / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q86WA6, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-MN / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-TYC / |
#5: 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: 3.4 Å3/Da / Density % sol: 63.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 15-16% PEG 4,000, 0.1 M MOPS, 0.1 M MNSO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9792 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 24, 2006 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→38.36 Å / Num. obs: 30385 / % possible obs: 99.6 % / Redundancy: 10.93 % / Rmerge(I) obs: 0.125 / Χ2: 0.96 / Net I/σ(I): 11.4 / Scaling rejects: 2509 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OCG Resolution: 1.9→38.36 Å / σ(F): 0 / Details: Friedel pairs were used in refinement
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Solvent computation | Bsol: 60.754 Å2 | ||||||||||||||||||||
Displacement parameters | Biso mean: 30.154 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→38.36 Å
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Refine LS restraints |
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Xplor file |
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