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- PDB-8q23: HsNMT1 in complex with both MyrCoA and Ac-D-ORN-SFSKPR inhibitor ... -

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Basic information

Entry
Database: PDB / ID: 8q23
TitleHsNMT1 in complex with both MyrCoA and Ac-D-ORN-SFSKPR inhibitor peptide
Components
  • ACE-ORD-SER-PHE-SER-LYS-PRO-ARG
  • Glycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / E-MYRISTOYLATION / NMT / MYRISTOYLTRANSFERASE TYPE1 / ACYLTRANSFERASE / GNAT / GCN5-RELATED N-ACETYLTRANSFERASES
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 / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / 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 / Activation, myristolyation of BID and translocation to mitochondria / positive regulation of establishment of protein localization to mitochondrion / glycylpeptide N-tetradecanoyltransferase / glycylpeptide N-tetradecanoyltransferase activity / protein localization to membrane / eNOS activation / 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
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
Similarity search - Domain/homology
TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDian, C. / Giglione, C. / Meinnel, T.
Funding support France, 4items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-20-CE44-0013 France
Agence Nationale de la Recherche (ANR)ANR-2010-BLAN-1611-01 France
Fondation ARCARCPJA32020060002137 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: Structure / Year: 2024
Title: Novel, tightly structurally related N-myristoyltransferase inhibitors display equally potent yet distinct inhibitory mechanisms.
Authors: Riviere, F. / Dian, C. / Dutheil, R.F. / Monassa, P. / Giglione, C. / Meinnel, T.
History
DepositionAug 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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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
I: ACE-ORD-SER-PHE-SER-LYS-PRO-ARG
E: ACE-ORD-SER-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,10912
Polymers94,6574
Non-polymers2,4528
Water11,097616
1
A: Glycylpeptide N-tetradecanoyltransferase 1
E: ACE-ORD-SER-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5266
Polymers47,3282
Non-polymers1,1984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-38 kcal/mol
Surface area16730 Å2
2
B: Glycylpeptide N-tetradecanoyltransferase 1
I: ACE-ORD-SER-PHE-SER-LYS-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5836
Polymers47,3282
Non-polymers1,2544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-24 kcal/mol
Surface area16670 Å2
Unit cell
Length a, b, c (Å)79.815, 179.102, 58.367
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABIE

#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: 46465.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NMT1, NMT / Details (production host): pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): ROSETTA2 PLYSS
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase
#2: Protein/peptide ACE-ORD-SER-PHE-SER-LYS-PRO-ARG


Mass: 863.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 624 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


Mass: 977.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H62N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 19% PEG6K, 0.1M Sodium citrate, 0.1 MgCl2, 0.1 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97563 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2020 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97563 Å / Relative weight: 1
ReflectionResolution: 1.9→48.9 Å / Num. obs: 127180 / % possible obs: 99.9 % / Redundancy: 14.9 % / Biso Wilson estimate: 25.77 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.021 / Rsym value: 0.08 / Net I/σ(I): 21.6
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 15 % / Mean I/σ(I) obs: 5 / Num. unique obs: 4263 / CC1/2: 0.966 / Rpim(I) all: 0.176 / Rsym value: 0.678 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 509T

509t


Resolution: 1.9→48.9 Å / SU ML: 0.1788 / Cross valid method: FREE R-VALUE / σ(F): 0.45 / Phase error: 20.2553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1948 6540 5.14 %
Rwork0.1578 120640 -
obs0.1597 127180 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6483 0 137 616 7236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076923
X-RAY DIFFRACTIONf_angle_d0.94049427
X-RAY DIFFRACTIONf_chiral_restr0.08411026
X-RAY DIFFRACTIONf_plane_restr0.00571193
X-RAY DIFFRACTIONf_dihedral_angle_d20.93862679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.27422390.22153944X-RAY DIFFRACTION99.81
1.92-1.940.26882190.20364089X-RAY DIFFRACTION99.22
1.94-1.970.31421690.20044011X-RAY DIFFRACTION99.74
1.97-1.990.23712290.18684028X-RAY DIFFRACTION99.91
1.99-2.020.21791880.18174081X-RAY DIFFRACTION99.35
2.02-2.050.24262370.18213940X-RAY DIFFRACTION99.83
2.05-2.080.24932470.17783996X-RAY DIFFRACTION99.86
2.08-2.110.23592450.17493985X-RAY DIFFRACTION99.58
2.11-2.140.22942030.17114013X-RAY DIFFRACTION99.95
2.14-2.170.19442490.174003X-RAY DIFFRACTION99.72
2.17-2.210.24232490.16423982X-RAY DIFFRACTION99.88
2.21-2.250.22932210.16554031X-RAY DIFFRACTION99.84
2.25-2.30.19572130.17274025X-RAY DIFFRACTION99.93
2.3-2.340.20022000.16374040X-RAY DIFFRACTION99.84
2.34-2.390.23251980.17124041X-RAY DIFFRACTION99.95
2.39-2.450.27361800.16984051X-RAY DIFFRACTION99.95
2.45-2.510.23012480.16414005X-RAY DIFFRACTION99.98
2.51-2.580.20962560.17584000X-RAY DIFFRACTION100
2.58-2.650.24492100.17664092X-RAY DIFFRACTION100
2.65-2.740.19991910.17134003X-RAY DIFFRACTION99.98
2.74-2.840.19832260.1644018X-RAY DIFFRACTION100
2.84-2.950.18831810.16714050X-RAY DIFFRACTION100
2.95-3.090.23452110.16194089X-RAY DIFFRACTION100
3.09-3.250.18942020.16164034X-RAY DIFFRACTION100
3.25-3.450.16732030.15134032X-RAY DIFFRACTION100
3.45-3.720.19062240.14143992X-RAY DIFFRACTION99.95
3.72-4.090.15852510.13653997X-RAY DIFFRACTION99.77
4.09-4.680.14222220.11884022X-RAY DIFFRACTION99.93
4.68-5.90.14362240.14144022X-RAY DIFFRACTION99.95
5.9-48.90.17842050.15884024X-RAY DIFFRACTION99.58

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