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- PDB-6fz3: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibi... -

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Basic information

Entry
Database: PDB / ID: 6fz3
TitleHuman N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibitor bound
ComponentsGlycylpeptide N-tetradecanoyltransferase 1
KeywordsTRANSFERASE / protein-ligand complex
Function / homology
Function and homology information


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 / 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-EBK / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKersten, F.C. / Brenk, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation252061573 Germany
CitationJournal: J.Med.Chem. / Year: 2020
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
DepositionMar 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)97,03910
Polymers93,8322
Non-polymers3,2078
Water3,261181
1
A: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5205
Polymers46,9161
Non-polymers1,6044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5205
Polymers46,9161
Non-polymers1,6044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.278, 58.000, 153.309
Angle α, β, γ (deg.)90.00, 92.18, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / 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: 0 / Auth seq-ID: 115 - 495 / Label seq-ID: 22 - 402

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 46915.855 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 (E. coli)
References: UniProt: P30419, glycylpeptide N-tetradecanoyltransferase

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Non-polymers , 5 types, 189 molecules

#2: Chemical ChemComp-EBK / 2,6-bis(chloranyl)-4-[2-(4-methylpiperazin-1-yl)pyridin-4-yl]-~{N}-(1,3,5-trimethylpyrazol-4-yl)benzenesulfonamide


Mass: 509.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26Cl2N6O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MYA / TETRADECANOYL-COA / MYRISTOYL-COA


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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 24% PEG 4000 5 mM NiCl2 0.1 M Na citrate 5% Glycerol

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDS0.5.436data reduction
pointless0.5.436data scaling
PHASERphasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FZ5

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
RfactorNum. reflection% reflectionSelection details
Rfree0.23492 2392 5.2 %RANDOM
Rwork0.19865 ---
obs0.20057 43570 84.46 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 27.798 Å2
Baniso -1Baniso -2Baniso -3
1-2.72 Å20 Å20.11 Å2
2---2.19 Å20 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 2→50.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 206 181 6481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196490
X-RAY DIFFRACTIONr_bond_other_d0.0020.025863
X-RAY DIFFRACTIONr_angle_refined_deg1.4561.9928868
X-RAY DIFFRACTIONr_angle_other_deg0.922313580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50724.014279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.855151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3261527
X-RAY DIFFRACTIONr_chiral_restr0.0820.2969
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021325
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_it1.2241.453059
X-RAY DIFFRACTIONr_mcbond_other1.2251.453058
X-RAY DIFFRACTIONr_mcangle_it2.0032.1673819
X-RAY DIFFRACTIONr_mcangle_other2.0022.1673820
X-RAY DIFFRACTIONr_scbond_it1.3391.5233431
X-RAY DIFFRACTIONr_scbond_other1.3391.5233431
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1212.2445049
X-RAY DIFFRACTIONr_long_range_B_refined3.50116.1776931
X-RAY DIFFRACTIONr_long_range_B_other3.49916.1276915
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24432 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 186 -
Rwork0.262 3326 -
obs--89.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0509-0.04780.19630.5396-0.00030.8652-0.0013-0.0066-0.0181-0.07710.0986-0.00550.00970.0626-0.09730.1847-0.05420.0040.128-0.02920.014711.0768.94556.445
20.0299-0.10910.1031.59140.08740.86410.0443-0.00620.0005-0.2819-0.18070.1979-0.1137-0.01230.13640.3185-0.006-0.07440.0695-0.02550.0449-8.90519.0721.24
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A110 - 1003
2X-RAY DIFFRACTION2B115 - 1003

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