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- PDB-7tux: Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-X... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tux | ||||||
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Title | Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with [(3S)-4-Hydroxy-3-[({2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl}methyl)amino]butyl]phosphonic acid | ||||||
![]() | Hypoxanthine-guanine-xanthine phosphoribosyltransferase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / inhibitors / drug design / transferase-inhibitor complex / Malaria / transition state analogs / transferase / Plasmodium falciparum / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage ...xanthine phosphoribosyltransferase / XMP salvage / xanthine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase / guanine salvage / hypoxanthine metabolic process / guanine phosphoribosyltransferase activity / hypoxanthine phosphoribosyltransferase activity / GMP salvage / IMP salvage / purine ribonucleoside salvage / nucleotide binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harijan, R.K. / Minnow, Y.V.T. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibition and Mechanism of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase. Authors: V T Minnow, Y. / Suthagar, K. / Clinch, K. / Ducati, R.G. / Ghosh, A. / Buckler, J.N. / Harijan, R.K. / Cahill, S.M. / Tyler, P.C. / Schramm, V.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.2 KB | Display | ![]() |
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PDB format | ![]() | 177.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ozfS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28410.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: LACZ / Production host: ![]() ![]() References: UniProt: P20035, xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase |
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-Non-polymers , 6 types, 825 molecules ![](data/chem/img/YBM.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-YBM / [( #3: Chemical | ChemComp-POP / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-ACY / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 200 mM Lithium Acetate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→173.65 Å / Num. obs: 128959 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.62→1.65 Å / Redundancy: 6 % / Rmerge(I) obs: 1.07 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6298 / CC1/2: 0.75 / % possible all: 99.8 |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3OZF Resolution: 1.62→57.47 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.413 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.06 Å2 / Biso mean: 25.517 Å2 / Biso min: 14.91 Å2
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Refinement step | Cycle: final / Resolution: 1.62→57.47 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.62→1.662 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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