+Open data
-Basic information
Entry | Database: PDB / ID: 8q8g | ||||||
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Title | Crystal structure of HsRNMT complexed with inhibitor DDD1870799 | ||||||
Components | mRNA cap guanine-N7 methyltransferase | ||||||
Keywords | RNA BINDING PROTEIN / Methyl transferase | ||||||
Function / homology | Function and homology information mRNA cap methyltransferase RNMT:RAMAC complex / mRNA capping enzyme complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity ...mRNA cap methyltransferase RNMT:RAMAC complex / mRNA capping enzyme complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / 7-methylguanosine mRNA capping / cellular response to leukemia inhibitory factor / fibrillar center / mRNA (guanine-N7)-methyltransferase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / receptor complex / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Petit, A.P. / Fyfe, P.K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Structure-Guided Design of HsRNMT inhibitors Authors: Petit, A.P. / Fyfe, P.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q8g.cif.gz | 155.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q8g.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 8q8g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q8g_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8q8g_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8q8g_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 8q8g_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/8q8g ftp://data.pdbj.org/pub/pdb/validation_reports/q8/8q8g | HTTPS FTP |
-Related structure data
Related structure data | 8q69C 8q9wC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 32550.559 Da / Num. of mol.: 2 / Mutation: 416-455 GLGC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNMT, KIAA0398 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O43148, mRNA (guanine-N7)-methyltransferase |
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-Non-polymers , 5 types, 117 molecules
#2: Chemical | #3: Chemical | Mass: 354.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19FN4O2 / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.11 Å3/Da / Density % sol: 41.65 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES pH 6.3-6.9, 50 mM Na2SO4, 18-25 % PEG 6000 PH range: 6.3-6.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 12, 2018 |
Radiation | Monochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.17 Å / Num. obs: 21196 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.4 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.156 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.853 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2207 / CC1/2: 0.57 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→42.17 Å / SU ML: 0.3525 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7755 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→42.17 Å
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Refine LS restraints |
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LS refinement shell |
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