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- PDB-6dtn: The structure of NTMT1 in complex with compound DC100-1 -

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Basic information

Entry
Database: PDB / ID: 6dtn
TitleThe structure of NTMT1 in complex with compound DC100-1
Components
  • (6D6)PPKRIA(NH2), DC100-1
  • N-terminal Xaa-Pro-Lys N-methyltransferase 1
Keywordstransferase/transferase inhibitor / methyltransferase / enzyme / inhibitor complex / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


N-terminal peptidyl-glycine methylation / N-terminal peptidyl-proline dimethylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation ...N-terminal peptidyl-glycine methylation / N-terminal peptidyl-proline dimethylation / N-terminal peptidyl-serine dimethylation / N-terminal peptidyl-serine trimethylation / protein N-terminal methyltransferase / N-terminal protein N-methyltransferase activity / protein methyltransferase activity / spindle organization / histone methyltransferase activity / chromosome segregation / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Alpha-N-methyltransferase NTM1 / AdoMet dependent proline di-methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(6D6)PPKRIA(NH2), DC100-1 / N-terminal Xaa-Pro-Lys N-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.475 Å
AuthorsNoinaj, N. / Chen, D. / Huang, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1U01CA214649-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM117275-01A1 United States
CitationJournal: J. Med. Chem. / Year: 2019
Title: Discovery of Bisubstrate Inhibitors for Protein N-Terminal Methyltransferase 1.
Authors: Chen, D. / Dong, G. / Noinaj, N. / Huang, R.
History
DepositionJun 18, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: N-terminal Xaa-Pro-Lys N-methyltransferase 1
A: (6D6)PPKRIA(NH2), DC100-1


Theoretical massNumber of molelcules
Total (without water)28,4072
Polymers28,4072
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-6 kcal/mol
Surface area11050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.166, 73.166, 82.361
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein N-terminal Xaa-Pro-Lys N-methyltransferase 1 / Alpha N-terminal protein methyltransferase 1A / Methyltransferase-like protein 11A / N-terminal ...Alpha N-terminal protein methyltransferase 1A / Methyltransferase-like protein 11A / N-terminal RCC1 methyltransferase / X-Pro-Lys N-terminal protein methyltransferase 1A / NTM1A


Mass: 27320.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NTMT1, C9orf32, METTL11A, NRMT, NRMT1, AD-003 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9BV86, protein N-terminal methyltransferase
#2: Protein/peptide (6D6)PPKRIA(NH2), DC100-1


Type: Oligopeptide / Class: Inhibitor / Mass: 1087.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: (6D6)PPKRIA(NH2), DC100-1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.5 M lithium sulfate; 0.1 M sodium HEPES 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.47→29.57 Å / Num. obs: 43110 / % possible obs: 99.3 % / Redundancy: 9.9 % / Rpim(I) all: 0.062 / Rrim(I) all: 0.142 / Rsym value: 0.128 / Net I/σ(I): 9.9
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 0.4 / Num. unique obs: 3067 / Rpim(I) all: 2.158 / Rrim(I) all: 4.939 / Rsym value: 4.433 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000denzodata reduction
HKL-2000scalepackdata scaling
PHASERwith PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E1M

5e1m


Resolution: 1.475→29.57 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1893 1988 4.64 %
Rwork0.1681 --
obs0.1691 42882 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.475→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 0 249 2174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111965
X-RAY DIFFRACTIONf_angle_d1.1872656
X-RAY DIFFRACTIONf_dihedral_angle_d24.468734
X-RAY DIFFRACTIONf_chiral_restr0.099293
X-RAY DIFFRACTIONf_plane_restr0.008342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4754-1.51230.34971300.36292710X-RAY DIFFRACTION92
1.5123-1.55320.3581350.32722866X-RAY DIFFRACTION98
1.5532-1.59890.33331430.3162876X-RAY DIFFRACTION99
1.5989-1.65050.34771390.29282861X-RAY DIFFRACTION99
1.6505-1.70950.2851420.28682906X-RAY DIFFRACTION99
1.7095-1.77790.30981430.24882918X-RAY DIFFRACTION99
1.7779-1.85880.2411410.19142899X-RAY DIFFRACTION99
1.8588-1.95680.19421410.1622912X-RAY DIFFRACTION99
1.9568-2.07940.19211470.14722944X-RAY DIFFRACTION99
2.0794-2.23990.16121390.14642925X-RAY DIFFRACTION100
2.2399-2.46520.16181420.14582955X-RAY DIFFRACTION100
2.4652-2.82160.19831440.15142995X-RAY DIFFRACTION100
2.8216-3.5540.1521500.14833000X-RAY DIFFRACTION100
3.554-29.57550.1581520.14823127X-RAY DIFFRACTION100

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