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- PDB-6fz2: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibi... -

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Basic information

Entry
Database: PDB / ID: 6fz2
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 / 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
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-31A / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsKersten, F.C. / Brenk, R. / Jaenicke, E.
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)96,75510
Polymers93,8322
Non-polymers2,9238
Water4,612256
1
A: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3785
Polymers46,9161
Non-polymers1,4624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3785
Polymers46,9161
Non-polymers1,4624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.530, 58.290, 153.900
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 116 - 496 / Label seq-ID: 23 - 403

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, 264 molecules

#2: Chemical ChemComp-31A / N-[2-(3-methoxyphenyl)ethanimidoyl]-2-piperidin-4-yloxy-benzamide


Mass: 367.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H25N3O3 / 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


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / 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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.05→16.8 Å / Num. obs: 51372 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 22.05 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.085 / Rrim(I) all: 0.164 / Net I/σ(I): 6.2
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3863 / CC1/2: 0.636 / Rpim(I) all: 0.414 / Rrim(I) all: 0.798 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDS0.5.436data reduction
pointless0.5.436data scaling
xia20.5.436data reduction
PHASERphasing
Coot0.8.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FZ5

6fz5


Resolution: 2.05→16.8 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.573 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.211
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 tlsd waters exclude ...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 tlsd waters exclude #Restraint weights weight MATRIX 0.02 temp 0.50 #NCS handling ncsr local ncsr align level 0.90 iterate N rmslevel 2.00 ncsr neighbours exclude
RfactorNum. reflection% reflectionSelection details
Rfree0.27786 2670 5.2 %RANDOM
Rwork0.23657 ---
obs0.23876 48702 99.19 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 32.57 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å2-0 Å2-0.3 Å2
2---3.66 Å2-0 Å2
3---1.73 Å2
Refinement stepCycle: 1 / Resolution: 2.05→16.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5976 0 194 256 6426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196334
X-RAY DIFFRACTIONr_bond_other_d0.0020.025754
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9828629
X-RAY DIFFRACTIONr_angle_other_deg0.9112.98813321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36723.564275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30115985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9661529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216877
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021316
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_it1.0691.5332986
X-RAY DIFFRACTIONr_mcbond_other1.0671.5332985
X-RAY DIFFRACTIONr_mcangle_it1.6792.2943725
X-RAY DIFFRACTIONr_mcangle_other1.6792.2943726
X-RAY DIFFRACTIONr_scbond_it1.1611.643348
X-RAY DIFFRACTIONr_scbond_other1.1611.643349
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7732.4214905
X-RAY DIFFRACTIONr_long_range_B_refined3.80318.0186847
X-RAY DIFFRACTIONr_long_range_B_other3.80318.0246848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23918 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 168 -
Rwork0.338 3689 -
obs--99.3 %
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)
10.61410.05510.12651.8755-0.16880.830.0132-0.0938-0.05010.20240.0029-0.11370.00260.0088-0.01610.1099-0.0108-0.01790.1869-0.00460.033110.70928.745755.7349
20.829-0.06150.21752.1001-0.22621.2833-0.02850.0801-0.0274-0.3455-0.03790.1401-0.075-0.09030.06640.20640.0199-0.02920.2259-0.02130.0166-8.896918.782221.6342
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A116 - 1003
2X-RAY DIFFRACTION2B116 - 1003

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