+Open data
-Basic information
Entry | Database: PDB / ID: 1bzy | ||||||
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Title | HUMAN HGPRTASE WITH TRANSITION STATE INHIBITOR | ||||||
Components | HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE | ||||||
Keywords | PHOSPHORIBOSYLTRANSFERASE / IMMUCILLIN / LESCH-NYHAN / HGPRT / TRANSITION STATE / MAGNESIUM / PYROPHOSPHATE / OXOCARBENIUM ION / NEIGHBORING GROUP PARTICIPATION | ||||||
Function / homology | Function and homology information adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase ...adenine metabolic process / Defective HPRT1 disrupts guanine and hypoxanthine salvage / GMP catabolic process / guanine salvage / hypoxanthine metabolic process / hypoxanthine salvage / cerebral cortex neuron differentiation / positive regulation of dopamine metabolic process / lymphocyte proliferation / hypoxanthine phosphoribosyltransferase / IMP metabolic process / GMP salvage / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / grooming behavior / IMP salvage / Purine salvage / striatum development / AMP salvage / dopaminergic neuron differentiation / purine nucleotide biosynthetic process / Azathioprine ADME / purine ribonucleoside salvage / dendrite morphogenesis / dopamine metabolic process / central nervous system neuron development / response to amphetamine / locomotory behavior / T cell mediated cytotoxicity / protein homotetramerization / nucleotide binding / magnesium ion binding / extracellular exosome / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shi, W. / Li, C. / Tyler, P.C. / Furneaux, R.H. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: The 2.0 A structure of human hypoxanthine-guanine phosphoribosyltransferase in complex with a transition-state analog inhibitor. Authors: Shi, W. / Li, C.M. / Tyler, P.C. / Furneaux, R.H. / Grubmeyer, C. / Schramm, V.L. / Almo, S.C. #1: Journal: Cell(Cambridge,Mass.) / Year: 1994 Title: The Crystal Structure of Human Hypoxanthine-Guanine Phosphoribosyltransferase with Bound Gmp Authors: Eads, J.C. / Scapin, G. / Xu, Y. / Grubmeyer, C. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bzy.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bzy.ent.gz | 150.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bzy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/1bzy ftp://data.pdbj.org/pub/pdb/validation_reports/bz/1bzy | HTTPS FTP |
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-Related structure data
Related structure data | 1dbrS 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 24481.217 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P00492, hypoxanthine phosphoribosyltransferase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-IMU / #4: Chemical | ChemComp-POP / #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: 1.9 Å3/Da / Density % sol: 35 % | ||||||||||||||||||||
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Crystal grow | pH: 4.6 / Details: pH 4.6 | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging dropDetails: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97946 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2→10 Å / Num. obs: 44301 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 15.4 Å2 / Rsym value: 0.045 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 8.3 / Rsym value: 0.2 / % possible all: 81 |
Reflection | *PLUS Num. measured all: 232173 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS % possible obs: 81 % / Rmerge(I) obs: 0.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DBR Resolution: 2→10 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 16.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
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