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Yorodumi- PDB-6fz2: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fz2 | ||||||
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Title | Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound | ||||||
Components | Glycylpeptide N-tetradecanoyltransferase 1 | ||||||
Keywords | TRANSFERASE / protein-ligand complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Kersten, F.C. / Brenk, R. / Jaenicke, E. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 Title: How To Design Selective Ligands for Highly Conserved Binding Sites: A Case Study UsingN-Myristoyltransferases as a Model System. Authors: Kersten, C. / Fleischer, E. / Kehrein, J. / Borek, C. / Jaenicke, E. / Sotriffer, C. / Brenk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fz2.cif.gz | 325.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fz2.ent.gz | 261.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fz/6fz2 ftp://data.pdbj.org/pub/pdb/validation_reports/fz/6fz2 | HTTPS FTP |
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-Related structure data
Related structure data | 6eu5C 6ewfC 6f56C 6fz3C 6fz5SC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 116 - 496 / Label seq-ID: 23 - 403
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46915.855 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Production host: Escherichia coli (E. coli) References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase |
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-Non-polymers , 5 types, 264 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.33 Å3/Da / Density % sol: 47.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 24% PEG 4000 5 mM NiCl2 0.1 M Na citrate 5% Glycerol |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→16.8 Å / Num. obs: 51372 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.085 / Rrim(I) all: 0.164 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3863 / CC1/2: 0.636 / Rpim(I) all: 0.414 / Rrim(I) all: 0.798 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FZ5 Resolution: 2.05→16.8 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.573 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.211 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS #B-factor model selection refi bref ISOT #Solvent related settings scal type SIMP lssc function a sigma n solvent YES tlsd waters exclude ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS #B-factor model selection refi bref ISOT #Solvent related settings scal type SIMP lssc function a sigma n solvent YES tlsd waters exclude #Restraint weights weight MATRIX 0.02 temp 0.50 #NCS handling ncsr local ncsr align level 0.90 iterate N rmslevel 2.00 ncsr neighbours exclude
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.57 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→16.8 Å
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Refine LS restraints |
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