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- PDB-5mu6: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and IMP-10... -

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Basic information

Entry
Database: PDB / ID: 5mu6
TitleHuman N-myristoyltransferase (NMT1) with Myristoyl-CoA and IMP-1088 inhibitor bound
ComponentsGlycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / N-myristoylation / Inhibitor / Rhinovirus capsule assembly
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 / positive regulation of establishment of protein localization to mitochondrion / Activation, myristolyation of BID and translocation to mitochondria / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity ...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 / positive regulation of establishment of protein localization to mitochondrion / 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
Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase ...Aminopeptidase - #170 / Glycylpeptide N-tetradecanoyltransferase, conserved site / Myristoyl-CoA:protein N-myristoyltransferase signature 1. / Myristoyl-CoA:protein N-myristoyltransferase signature 2. / Glycylpeptide N-tetradecanoyltransferase / Glycylpeptide N-tetradecanoyltransferase, N-terminal / Glycylpeptide N-tetradecanoyltransferase, C-terminal / Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain / Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KFK / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsPerez-Dorado, I. / Bell, A.S. / Tate, E.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
CitationJournal: Nat Chem / Year: 2018
Title: Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus.
Authors: Mousnier, A. / Bell, A.S. / Swieboda, D.P. / Morales-Sanfrutos, J. / Perez-Dorado, I. / Brannigan, J.A. / Newman, J. / Ritzefeld, M. / Hutton, J.A. / Guedan, A. / Asfor, A.S. / Robinson, S.W. ...Authors: Mousnier, A. / Bell, A.S. / Swieboda, D.P. / Morales-Sanfrutos, J. / Perez-Dorado, I. / Brannigan, J.A. / Newman, J. / Ritzefeld, M. / Hutton, J.A. / Guedan, A. / Asfor, A.S. / Robinson, S.W. / Hopkins-Navratilova, I. / Wilkinson, A.J. / Johnston, S.L. / Leatherbarrow, R.J. / Tuthill, T.J. / Solari, R. / Tate, E.W.
History
DepositionJan 12, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycylpeptide N-tetradecanoyltransferase 1
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,18712
Polymers90,9072
Non-polymers3,28010
Water8,215456
1
A: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0936
Polymers45,4531
Non-polymers1,6405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0936
Polymers45,4531
Non-polymers1,6405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.730, 180.730, 58.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycylpeptide N-tetradecanoyltransferase 1 / Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N- ...Myristoyl-CoA:protein N-myristoyltransferase 1 / Type I N-myristoyltransferase / Peptide N-myristoyltransferase 1


Mass: 45453.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Plasmid: pET-28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pRareS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 5 types, 466 molecules

#2: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H62N7O17P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-KFK / 1-[5-[3,4-bis(fluoranyl)-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-1-methyl-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine


Mass: 453.527 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29F2N5O / Comment: inhibitor*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 23% (v/w) MME2K, 0.2M KBr, 100 mM sodium citrate pH 4.5, and 5% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.88→72.18 Å / Num. obs: 69366 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 13.1 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.254 / Rpim(I) all: 0.101 / Net I/σ(I): 7.8
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.654 / Num. unique all: 5068 / Num. unique obs: 5068 / CC1/2: 0.501 / Rpim(I) all: 0.716 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.17data scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PHENIX1.8.4_1496refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C2Y

4c2y


Resolution: 1.88→72.179 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.69
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 3449 4.98 %Random
Rwork0.2038 ---
obs0.206 69279 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.82 Å2
Refinement stepCycle: LAST / Resolution: 1.88→72.179 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6230 0 218 456 6904
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086670
X-RAY DIFFRACTIONf_angle_d1.2429078
X-RAY DIFFRACTIONf_dihedral_angle_d14.5492516
X-RAY DIFFRACTIONf_chiral_restr0.051973
X-RAY DIFFRACTIONf_plane_restr0.0051130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.90580.36621450.31612578X-RAY DIFFRACTION100
1.9058-1.9330.37711500.31132597X-RAY DIFFRACTION100
1.933-1.96180.34841250.29482608X-RAY DIFFRACTION99
1.9618-1.99250.33121210.28382559X-RAY DIFFRACTION99
1.9925-2.02520.29261200.25512646X-RAY DIFFRACTION100
2.0252-2.06010.32821270.25712592X-RAY DIFFRACTION100
2.0601-2.09760.29061400.23582617X-RAY DIFFRACTION100
2.0976-2.13790.29031340.25052611X-RAY DIFFRACTION100
2.1379-2.18160.29521410.23562631X-RAY DIFFRACTION100
2.1816-2.2290.26471510.24162532X-RAY DIFFRACTION100
2.229-2.28080.25691180.22552645X-RAY DIFFRACTION100
2.2808-2.33790.26181630.22612589X-RAY DIFFRACTION100
2.3379-2.40110.25371370.22242621X-RAY DIFFRACTION99
2.4011-2.47180.31411370.21762622X-RAY DIFFRACTION100
2.4718-2.55150.27961400.21852601X-RAY DIFFRACTION100
2.5515-2.64270.27121210.21282631X-RAY DIFFRACTION100
2.6427-2.74860.26591330.20242638X-RAY DIFFRACTION100
2.7486-2.87370.26141430.20852642X-RAY DIFFRACTION100
2.8737-3.02520.26971360.20662646X-RAY DIFFRACTION100
3.0252-3.21470.24961390.20182636X-RAY DIFFRACTION100
3.2147-3.46290.22511410.17692679X-RAY DIFFRACTION100
3.4629-3.81140.22611510.1652646X-RAY DIFFRACTION100
3.8114-4.36280.16351380.14752693X-RAY DIFFRACTION100
4.3628-5.49640.14921340.14652728X-RAY DIFFRACTION100
5.4964-72.2320.20991640.17992842X-RAY DIFFRACTION100

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