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Yorodumi- PDB-3zno: IN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: RE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zno | ||||||
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Title | IN VITRO AND IN VIVO INHIBITION OF HUMAN D-AMINO ACID OXIDASE: REGULATION OF D-SERINE CONCENTRATION IN THE BRAIN | ||||||
Components | D-AMINO-ACID OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / NEUROTRANSMISSION | ||||||
Function / homology | Function and homology information D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / digestion ...D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / digestion / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / FAD binding / cell projection / Peroxisomal protein import / extracellular region / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. ...Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. / Foglesong, R.J. / Soukri, M. / Chytil, M. / Fang, Q.K. / Jones, S.W. / Varney, M.A. / Panatier, A. / Oliet, S.H.R. / Pollegioni, L. / Piubelli, L. / Molla, G. / Nardini, M. / Large, T.H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Structural, Kinetic, and Pharmacodynamic Mechanisms of D-Amino Acid Oxidase Inhibition by Small Molecules. Authors: Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. / Foglesong, R.J. / Soukri, M. / Chytil, M. ...Authors: Hopkins, S.C. / Heffernan, M.L.R. / Saraswat, L.D. / Bowen, C.A. / Melnick, L. / Hardy, L.W. / Orsini, M.A. / Allen, M.S. / Koch, P. / Spear, K.L. / Foglesong, R.J. / Soukri, M. / Chytil, M. / Fang, Q.K. / Jones, S.W. / Varney, M.A. / Panatier, A. / Oliet, S.H.R. / Pollegioni, L. / Piubelli, L. / Molla, G. / Nardini, M. / Large, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zno.cif.gz | 302.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zno.ent.gz | 244.8 KB | Display | PDB format |
PDBx/mmJSON format | 3zno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zno_validation.pdf.gz | 941.6 KB | Display | wwPDB validaton report |
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Full document | 3zno_full_validation.pdf.gz | 963.9 KB | Display | |
Data in XML | 3zno_validation.xml.gz | 31.5 KB | Display | |
Data in CIF | 3zno_validation.cif.gz | 43.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/3zno ftp://data.pdbj.org/pub/pdb/validation_reports/zn/3zno | HTTPS FTP |
-Related structure data
Related structure data | 3znnC 3znpC 3znqC 2du8S 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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Unit cell |
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-Components
#1: Protein | Mass: 39520.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14920, D-amino-acid oxidase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.21 Å3/Da / Density % sol: 44.3 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 |
Detector | Type: RIGAKU SATURN / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→64.93 Å / Num. obs: 29214 / % possible obs: 90.6 % / Observed criterion σ(I): 2 / Redundancy: 4.21 % / Biso Wilson estimate: 47.06 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DU8 Resolution: 2.3→39.25 Å / Cor.coef. Fo:Fc: 0.9196 / Cor.coef. Fo:Fc free: 0.8633 / SU R Cruickshank DPI: 0.536 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.606 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.309 Details: RESIDUES A296-A303, A338-A340 B303, B338-B340 ARE DISORDERED. POOR DENSITY IS PRESENT FOR RESIDUES A296, A297, A298, A299, A300, A301, A302, A303, A338, A339, A340, B55,B56, B57, B58, B59, ...Details: RESIDUES A296-A303, A338-A340 B303, B338-B340 ARE DISORDERED. POOR DENSITY IS PRESENT FOR RESIDUES A296, A297, A298, A299, A300, A301, A302, A303, A338, A339, A340, B55,B56, B57, B58, B59, B60, B61, B162, B163, B296, B297, B298, B299, B300, B301, B302, B303, B338, B339, B340 FINAL STRUCTURE HAS NO RESIDUES IN THE DISALLOWED REGION OF THE RAMACHANDRAN PLOT AS DEFINED IN THE CCP4 PROCHECK PROGRAM.
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Displacement parameters | Biso mean: 51.43 Å2
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Refine analyze | Luzzati coordinate error obs: 0.332 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→39.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 15
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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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