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- PDB-6fz3: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fz3 | ||||||
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Title | Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound | ||||||
![]() | Glycylpeptide N-tetradecanoyltransferase 1 | ||||||
![]() | TRANSFERASE / protein-ligand complex | ||||||
Function / homology | ![]() 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kersten, F.C. / Brenk, R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 328.7 KB | Display | ![]() |
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PDB format | ![]() | 265.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 31.1 KB | Display | |
Data in CIF | ![]() | 42.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6eu5C ![]() 6ewfC ![]() 6f56C ![]() 6fz2C ![]() 6fz5SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 115 - 495 / Label seq-ID: 22 - 402
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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.) ![]() ![]() ![]() References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase |
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-Non-polymers , 5 types, 189 molecules ![](data/chem/img/EBK.gif)
![](data/chem/img/MYA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MYA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976251 Å / Relative weight: 1 |
Reflection | Resolution: 2→76.6 Å / Num. obs: 46006 / % possible obs: 84.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 15.92 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.08 / Rrim(I) all: 0.129 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3522 / CC1/2: 0.806 / Rpim(I) all: 0.308 / Rrim(I) all: 0.498 / % possible all: 89.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6FZ5 Resolution: 2→50.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 11.894 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.195 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 solvent vdwprobe 1.1 ...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 solvent vdwprobe 1.1 ionprobe 0.7 rshrink 0.7 tlsd waters exclude #Restraint weights weight MATRIX 0.027777 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: 27.798 Å2
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Refinement step | Cycle: 1 / Resolution: 2→50.87 Å
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Refine LS restraints |
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