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- PDB-6fz5: Human N-myristoyltransferase (NMT1) with Myristoyl-CoA and inhibi... -

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Basic information

Entry
Database: PDB / ID: 6fz5
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-BXN / TETRADECANOYL-COA / Glycylpeptide N-tetradecanoyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 14, 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

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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)92,37012
Polymers88,9692
Non-polymers3,40210
Water6,936385
1
A: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1856
Polymers44,4841
Non-polymers1,7015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycylpeptide N-tetradecanoyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1856
Polymers44,4841
Non-polymers1,7015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.390, 58.160, 154.001
Angle α, β, γ (deg.)90.00, 92.36, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A115 - 496
2010B115 - 496

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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: 44484.277 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, 395 molecules

#2: Chemical ChemComp-BXN / 4-[3-[(8~{a}~{R})-3,4,6,7,8,8~{a}-hexahydro-1~{H}-pyrrolo[1,2-a]pyrazin-2-yl]propyl]-2,6-bis(chloranyl)-~{N}-methyl-~{N}-(1,3,5-trimethylpyrazol-4-yl)benzenesulfonamide


Mass: 514.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H33Cl2N5O2S / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
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: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.89→76.94 Å / Num. obs: 62185 / % possible obs: 94.8 % / Redundancy: 2.6 % / Biso Wilson estimate: 22.42 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.061 / Rrim(I) all: 0.105 / Net I/σ(I): 6.4
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4069 / CC1/2: 0.605 / Rpim(I) all: 0.403 / Rrim(I) all: 0.687 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
PDB_EXTRACT3.22data extraction
MOSFLM7.2.1data reduction
pointless1.11.4data scaling
Coot0.8.2model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→76.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.986 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.148
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 1.0 ...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 1.0 ionprobe 0.7 rshrink 0.7 tlsd waters exclude #Restraint weights weight MATRIX 0.03 temp 0.50 #NCS handling ncsr local ncsr align level 0.90 iterate N rmslevel 2.00 ncsr neighbours exclude
RfactorNum. reflection% reflectionSelection details
Rfree0.22339 3212 5.2 %RANDOM
Rwork0.18936 ---
obs0.19115 58973 94.35 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 33.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20.54 Å2
2---0.36 Å2-0 Å2
3---0.57 Å2
Refinement stepCycle: 1 / Resolution: 1.89→76.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6116 0 218 385 6719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196525
X-RAY DIFFRACTIONr_bond_other_d0.0020.025960
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9948903
X-RAY DIFFRACTIONr_angle_other_deg0.913313834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2655763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83824.036280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.969151035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3351526
X-RAY DIFFRACTIONr_chiral_restr0.0820.2971
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217039
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021315
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_it1.1421.443047
X-RAY DIFFRACTIONr_mcbond_other1.1421.443048
X-RAY DIFFRACTIONr_mcangle_it1.8472.1513805
X-RAY DIFFRACTIONr_mcangle_other1.8472.1523806
X-RAY DIFFRACTIONr_scbond_it1.4691.6183478
X-RAY DIFFRACTIONr_scbond_other1.4661.6183478
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2932.3765097
X-RAY DIFFRACTIONr_long_range_B_refined5.00317.497126
X-RAY DIFFRACTIONr_long_range_B_other4.95917.1027047
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 24970 / 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: 1.888→1.937 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 209 -
Rwork0.317 4471 -
obs--96.49 %
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)
10.50410.1371-0.07512.2562-0.16651.00430.051-0.1809-0.02330.2662-0.0092-0.14470.01740.1175-0.04190.2434-0.0088-0.12810.07450.00020.068511.078.84756.287
20.8943-0.10150.06192.2452-0.10251.3258-0.01450.096-0.0696-0.3558-0.04290.2557-0.0775-0.15150.05750.31860.0234-0.14820.0304-0.02340.0798-9.03319.15421.044
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A115 - 1004
2X-RAY DIFFRACTION2B115 - 1004

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