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Yorodumi- PDB-4c2z: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c2z | ||||||
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Title | Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound | ||||||
Components | GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1 | ||||||
Keywords | TRANSFERASE / MYRISTOYLATION | ||||||
Function / homology | Function and homology information myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular 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 / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular 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) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.08 Å | ||||||
Authors | Thinon, E. / Serwa, R.A. / Brannigan, J.A. / Brassat, U. / Wright, M.H. / Heal, W.P. / Wilkinson, A.J. / Mann, D.J. / Tate, E.W. | ||||||
Citation | Journal: Nat.Commun. / Year: 2014 Title: Chemical Proteomics Defines the Mammalian N- Myristoylated Proteome in Live Cells Global Profiling of Co- and Post-Translationally N-Myristoylated Proteomes in Human Cells. Authors: Thinon, E. / Serwa, R.A. / Broncel, M. / Brannigan, J.A. / Brassat, U. / Wright, M.H. / Heal, W.P. / Wilkinson, A.J. / Mann, D.J. / Tate, E.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c2z.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c2z.ent.gz | 155.2 KB | Display | PDB format |
PDBx/mmJSON format | 4c2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/4c2z ftp://data.pdbj.org/pub/pdb/validation_reports/c2/4c2z | HTTPS FTP |
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-Related structure data
-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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47605.688 Da / Num. of mol.: 2 / Fragment: RESIDUES 109-496 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 DERIVATIVE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PRARE References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase |
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-Non-polymers , 7 types, 557 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CL / #8: 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: 2.26 Å3/Da / Density % sol: 45.5 % / Description: NONE |
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Crystal grow | pH: 4.5 Details: 25% PEG 2000 MME, 0.2 M KBR, 100 MM NA CITRATE PH 4.5, 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9783 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9783 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→89 Å / Num. obs: 50468 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.08→2.14 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 2.08→89.56 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.388 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.196 / 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 mean: 25.93 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→89.56 Å
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