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Yorodumi- PDB-1hmp: THE CRYSTAL STRUCTURE OF HUMAN HYPOXANTHINE-GUANINE PHOSPHORIBOSY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hmp | ||||||
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Title | THE CRYSTAL STRUCTURE OF HUMAN HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE WITH BOUND GMP | ||||||
Components | HYPOXANTHINE GUANINE PHOSPHORIBOSYL-TRANSFERASE | ||||||
Keywords | TRANSFERASE (GLYCOSYLTRANSFERASE) | ||||||
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 / Resolution: 2.5 Å | ||||||
Authors | Eads, J.C. / Scapin, G. / Xu, Y. / Grubmeyer, C. / Sacchettini, J.C. | ||||||
Citation | 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. #1: Journal: Biochemistry / Year: 1994 Title: Crystal Structure of Orotate Phosphoribosyltransferase Authors: Scapin, G. / 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 | 1hmp.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hmp.ent.gz | 74.6 KB | Display | PDB format |
PDBx/mmJSON format | 1hmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/1hmp ftp://data.pdbj.org/pub/pdb/validation_reports/hm/1hmp | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24481.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) References: UniProt: P00492, hypoxanthine phosphoribosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | THE HET GROUP HAS A CHARGE OF 1- AT PH 5.6. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.45 Å / Num. obs: 16428 / % possible obs: 85 % / Rmerge(I) obs: 0.07 |
-Processing
Software |
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Refinement | Resolution: 2.5→20 Å / σ(F): 1 Details: A LOOP OF RESIDUES 103 - 121 IN BOTH CHAINS A AND B IS POORLY ORDERED. COORDINATES GIVEN FOR THIS REGION RESULT FROM A TENTATIVE FITTING TO POOR ELECTRON DENSITY AND SHOULD BE TREATED WITH ...Details: A LOOP OF RESIDUES 103 - 121 IN BOTH CHAINS A AND B IS POORLY ORDERED. COORDINATES GIVEN FOR THIS REGION RESULT FROM A TENTATIVE FITTING TO POOR ELECTRON DENSITY AND SHOULD BE TREATED WITH CAUTION. FOR THIS LOOP IN THE SECOND MONOMER, RESIDUES 105 - 108 AND 121 ARE MISSING. SOME RESIDUES IN THIS REGION ARE MODELED AS ALANINE RESIDUES.
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |