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- PDB-5o9u: HsNMT1 in complex with CoA and Myristoylated-GCSVSKKK octapeptide -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o9u | |||||||||
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Title | HsNMT1 in complex with CoA and Myristoylated-GCSVSKKK octapeptide | |||||||||
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![]() | TRANSFERASE / GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1 N-MYRISTOYLTRANSFERASE 1 / N-MYRISTOYLTRANSFERASE TYPE1 / NMT1 / NMT / ACYLTRANSFERASE / MYR-PEPTIDE / COA / MYR-COA / MYRISTOYL / GNAT | |||||||||
Function / homology | ![]() hypotonic salinity response / calcium-dependent protein serine/threonine phosphatase activity / myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / calcineurin complex / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria ...hypotonic salinity response / calcium-dependent protein serine/threonine phosphatase activity / myristoyltransferase activity / peptidyl-lysine N6-myristoyltransferase activity / N-terminal peptidyl-glycine N-myristoylation / Late Phase of HIV Life Cycle / cellular ketone metabolic process / calcineurin complex / regulation of opsin-mediated signaling pathway / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / intracellular potassium ion homeostasis / protein localization to membrane / detection of calcium ion / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / calcium-mediated signaling / kinase binding / Inactivation, recovery and regulation of the phototransduction cascade / in utero embryonic development / calcium ion binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dian, C. / Meinnel, T. / Giglione, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and genomic decoding of human and plant myristoylomes reveals a definitive recognition pattern. Authors: Castrec, B. / Dian, C. / Ciccone, S. / Ebert, C.L. / Bienvenut, W.V. / Le Caer, J.P. / Steyaert, J.M. / Giglione, C. / Meinnel, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.1 KB | Display | ![]() |
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PDB format | ![]() | 157.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 41.5 KB | Display | |
Data in CIF | ![]() | 62.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o9sC ![]() 5o9tC ![]() 5o9vC ![]() 4c2zS S: Starting model for refinement C: citing same article ( |
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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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Components
-Protein / Protein/peptide , 2 types, 4 molecules ABCD
#1: Protein | Mass: 46465.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase #2: Protein/peptide | Mass: 839.036 Da / Num. of mol.: 2 / Fragment: UNP residues 2-9 / Source method: obtained synthetically Details: Synthetic octapeptide GCSVSKKK modified by NMT1 to (GLM)CSVSKKK. GLM: N-Myristoyl-glycine Source: (synth.) ![]() ![]() |
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-Non-polymers , 4 types, 919 molecules ![](data/chem/img/COA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MYR.gif)
![](data/chem/img/HOH.gif)
#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: 2.18 Å3/Da / Density % sol: 43.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 21% PEG 6000, 0.1M sodium citrate pH 5.6, 0.1M magnesium chloride, 0.1M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Oxford Cryo |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2016 / Details: Compound Refractive Lens |
Radiation | Monochromator: Diamond (C110) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→47.74 Å / Num. obs: 71441 / % possible obs: 99.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 13.51 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.046 / Rsym value: 0.073 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 5.5 / Num. unique obs: 6884 / CC1/2: 0.955 / Rpim(I) all: 0.171 / Rsym value: 0.266 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4C2Z Resolution: 1.85→47.037 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→47.037 Å
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Refine LS restraints |
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LS refinement shell |
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