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Yorodumi- PDB-1p4r: Crystal Structure of Human ATIC in complex with folate-based inhi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p4r | ||||||
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Title | Crystal Structure of Human ATIC in complex with folate-based inhibitor BW1540U88UD | ||||||
Components | Bifunctional purine biosynthesis protein PURH | ||||||
Keywords | TRANSFERASE / HYDROLASE / antifolate / ATIC / purine biosynthesis / BW1540U88UD | ||||||
Function / homology | Function and homology information phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / cellular response to interleukin-7 ...phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / GMP biosynthetic process / cellular response to interleukin-7 / nucleobase-containing compound metabolic process / dihydrofolate metabolic process / 'de novo' IMP biosynthetic process / Signaling by ALK fusions and activated point mutants / response to inorganic substance / animal organ regeneration / tetrahydrofolate biosynthetic process / cerebellum development / cerebral cortex development / cadherin binding / protein homodimerization activity / extracellular exosome / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Cheong, C.-G. / Greasley, S.E. / Horton, P.A. / Beardsley, G.P. / Wilson, I.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structures of human bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase/IMP cyclohydrolase in complex with potent sulfonyl-containing antifolates Authors: Cheong, C.-G. / Wolan, D.W. / Greasley, S.E. / Horton, P.A. / Beardsley, G.P. / Wilson, I.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p4r.cif.gz | 244.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p4r.ent.gz | 193.5 KB | Display | PDB format |
PDBx/mmJSON format | 1p4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p4/1p4r ftp://data.pdbj.org/pub/pdb/validation_reports/p4/1p4r | HTTPS FTP |
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-Related structure data
Related structure data | 1pl0C 1g8mS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 64693.719 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATIC cDNA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner DE3 References: UniProt: P31939, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase |
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-Non-polymers , 5 types, 406 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-XMP / | #6: 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: 2.41 Å3/Da / Density % sol: 48.52 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG3000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 83 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. obs: 42466 / Redundancy: 3.8 % / Rsym value: 0.11 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.55→2.64 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.489 / % possible all: 100 |
Reflection | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 4156 / Rmerge(I) obs: 0.489 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G8M Resolution: 2.55→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.55→30 Å
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Refine LS restraints |
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Xplor file |
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