+Open data
-Basic information
Entry | Database: PDB / ID: 6hmm | ||||||
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Title | POLYADPRIBOSYL GLYCOHYDROLASE IN COMPLEX WITH PDD00013907 | ||||||
Components | Poly(ADP-ribose) glycohydrolase | ||||||
Keywords | HYDROLASE / COMPETITIVE INHIBITOR / PARG | ||||||
Function / homology | Function and homology information nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix ...nucleotide-sugar metabolic process / poly(ADP-ribose) glycohydrolase / poly(ADP-ribose) glycohydrolase activity / ATP generation from poly-ADP-D-ribose / POLB-Dependent Long Patch Base Excision Repair / regulation of DNA repair / base-excision repair, gap-filling / carbohydrate metabolic process / nuclear body / mitochondrial matrix / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Tucker, J.A. / Brassington, C. / Hassall, G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2018 Title: Cell-Active Small Molecule Inhibitors of the DNA-Damage Repair Enzyme Poly(ADP-ribose) Glycohydrolase (PARG): Discovery and Optimization of Orally Bioavailable Quinazolinedione Sulfonamides. Authors: Waszkowycz, B. / Smith, K.M. / McGonagle, A.E. / Jordan, A.M. / Acton, B. / Fairweather, E.E. / Griffiths, L.A. / Hamilton, N.M. / Hamilton, N.S. / Hitchin, J.R. / Hutton, C.P. / James, D.I. ...Authors: Waszkowycz, B. / Smith, K.M. / McGonagle, A.E. / Jordan, A.M. / Acton, B. / Fairweather, E.E. / Griffiths, L.A. / Hamilton, N.M. / Hamilton, N.S. / Hitchin, J.R. / Hutton, C.P. / James, D.I. / Jones, C.D. / Jones, S. / Mould, D.P. / Small, H.F. / Stowell, A.I.J. / Tucker, J.A. / Waddell, I.D. / Ogilvie, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hmm.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hmm.ent.gz | 99.4 KB | Display | PDB format |
PDBx/mmJSON format | 6hmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/6hmm ftp://data.pdbj.org/pub/pdb/validation_reports/hm/6hmm | HTTPS FTP |
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-Related structure data
Related structure data | 6hmkC 6hmlC 6hmnC 4a0dS 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, 1 molecules A
#1: Protein | Mass: 60976.258 Da / Num. of mol.: 1 / Mutation: K616A, Q617A, K618A, E688A, K689A, K690A Source method: isolated from a genetically manipulated source Details: Cysteines 268 and 500 have become singly oxidised during purification/ crystallisation (ie microheterogeneity) Source: (gene. exp.) Homo sapiens (human) / Gene: PARG / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD References: UniProt: Q86W56, poly(ADP-ribose) glycohydrolase |
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-Non-polymers , 5 types, 532 molecules
#2: Chemical | ChemComp-DMS / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-7JB / ~{ | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Mix purified protein in 50 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM DTT at 7.5 mg/mL with a precipitant consisting of 28% PEG-3350, 0.2 M magnesium chloride, 0.1 M PCTP (0.04 M sodium propionate, ...Details: Mix purified protein in 50 mM HEPES, pH 7.0, 150 mM NaCl, 2 mM DTT at 7.5 mg/mL with a precipitant consisting of 28% PEG-3350, 0.2 M magnesium chloride, 0.1 M PCTP (0.04 M sodium propionate, 0.02 M sodium cacodylate, 0.04 M Bis-Tris propane) pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 15, 2010 / Details: Rigaku VariMaxHF |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→95.41 Å / Num. obs: 45150 / % possible obs: 95.7 % / Redundancy: 4.7 % / Biso Wilson estimate: 26.42 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.89→1.99 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2 / Num. unique all: 2509 / % possible all: 78.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4A0D Resolution: 1.9→27.8 Å / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.162
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Displacement parameters | Biso mean: 29.59 Å2
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Refine analyze | Luzzati coordinate error obs: 0.307 Å | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→27.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å
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