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- PDB-5o6j: Human NMT1 in complex with myristoyl-CoA and inhibitor IMP-1031 -

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Basic information

Entry
Database: PDB / ID: 5o6j
TitleHuman NMT1 in complex with myristoyl-CoA and inhibitor IMP-1031
ComponentsGlycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / Myristoyl / inhibitor
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-9M8 / TETRADECANOYL-COA / PHOSPHATE ION / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsBrannigan, J.A. / Wilkinson, A.J.
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
DepositionJun 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 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)94,35214
Polymers90,9072
Non-polymers3,44512
Water14,772820
1
A: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1767
Polymers45,4531
Non-polymers1,7236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1767
Polymers45,4531
Non-polymers1,7236
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.918, 177.285, 58.298
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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRareS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 5 types, 832 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-9M8 / 1-[5-[3-fluoranyl-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-1-methyl-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine


Mass: 435.537 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H30FN5O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 820 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.4M Sodium phosphate buffer, 17.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→80 Å / Num. obs: 145112 / % possible obs: 98.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 12.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Net I/σ(I): 15.2
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6950 / CC1/2: 0.766 / Rpim(I) all: 0.557 / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5O6H

5o6h


Resolution: 1.45→80 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.203 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.086 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24416 7227 5 %RANDOM
Rwork0.21346 ---
obs0.21502 136923 97.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.092 Å2
Baniso -1Baniso -2Baniso -3
1-2.56 Å20 Å20 Å2
2---0.81 Å2-0 Å2
3----1.75 Å2
Refinement stepCycle: 1 / Resolution: 1.45→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6281 0 222 820 7323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0197105
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3511.9969757
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3365883
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88423.864339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.099151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1281546
X-RAY DIFFRACTIONr_chiral_restr0.1630.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0215434
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9511.7413193
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.6222.6114020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6941.973911
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.42224.70411431
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 494 -
Rwork0.354 9838 -
obs--96.14 %

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