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Yorodumi- PDB-8q3d: HsNMT1 in complex with both MyrCoA and GNCFSKPR(NH2) inhibitor peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q3d | |||||||||||||||
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Title | HsNMT1 in complex with both MyrCoA and GNCFSKPR(NH2) inhibitor peptide | |||||||||||||||
Components |
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Keywords | TRANSFERASE / E-MYRISTOYLATION / NMT / MYRISTOYLTRANSFERASE TYPE1 / ACYLTRANSFERASE / GNAT / GCN5-RELATED N-ACETYLTRANSFERASES | |||||||||||||||
Function / homology | Function and homology information myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane ...myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / peptidyl-lysine N6-myristoyltransferase activity / Late Phase of HIV Life Cycle / ketone metabolic process / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Inactivation, recovery and regulation of the phototransduction cascade / in utero embryonic development / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) unidentified (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | |||||||||||||||
Authors | Dian, C. / Giglione, C. / Meinnel, T. | |||||||||||||||
Funding support | France, 4items
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Citation | Journal: to be published Title: HsNMT1 in complex with both MyrCoA and GNCFSKPR(NH2) inhibitor peptide Authors: Dian, C. / Giglione, C. / Meinnel, T. / Riviere, F. / Dutheil, F.R. / Monassa, P. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q3d.cif.gz | 236.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q3d.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8q3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q3d_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8q3d_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8q3d_validation.xml.gz | 37.3 KB | Display | |
Data in CIF | 8q3d_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q3/8q3d ftp://data.pdbj.org/pub/pdb/validation_reports/q3/8q3d | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Glycylpeptide N-tetradecanoyltransferase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 46408.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30419 |
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#2: Protein | Mass: 46407.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30419 |
-Protein/peptide , 1 types, 2 molecules CD
#3: Protein/peptide | Mass: 909.068 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) unidentified (others) / Production host: synthetic construct (others) |
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-Non-polymers , 5 types, 596 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Chemical | #8: 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: 2.19 Å3/Da / Density % sol: 43.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M MgCl2, 0.2 M NaCl, 0.1 M sodium citrate pH 5.6, and 18-24% (w/v) PEG 6K or 8K PH range: 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→48.78 Å / Num. obs: 45961 / % possible obs: 99.4 % / Redundancy: 17 % / Biso Wilson estimate: 18.73 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rsym value: 0.082 / Net I/σ(I): 29.3 |
Reflection shell | Resolution: 2.15→2.21 Å / Mean I/σ(I) obs: 13 / Num. unique obs: 3507 / CC1/2: 0.984 / Rpim(I) all: 0.066 / Rsym value: 0.262 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→47.67 Å / SU ML: 0.1781 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 17.351 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.61 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→47.67 Å
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Refine LS restraints |
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LS refinement shell |
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