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- PDB-9gvm: NNMT-SAH IN COMPLEX WITH 20p -

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Basic information

Entry
Database: PDB / ID: 9gvm
TitleNNMT-SAH IN COMPLEX WITH 20p
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / NNMT / SAM / SAH
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide N-methyltransferase activity / nicotinamide metabolic process / positive regulation of protein deacetylation / Metabolism of ingested SeMet, Sec, MeSec into H2Se / Methylation / : / positive regulation of gluconeogenesis / methylation / cytosol
Similarity search - Function
Methyltransferase, NNMT/PNMT/TEMT / Methyltransferase NNMT/PNMT/TEMT, conserved site / : / NNMT/PNMT/TEMT family / NNMT/PNMT/TEMT family of methyltransferases signature. / SAM-dependent methyltransferase NNMT/PNMT/TEMT-type profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsJohansson, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Not funded Sweden
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Mechanism and kinetics of turnover inhibitors of nicotinamide N-methyl transferase in vitro and in vivo.
Authors: Akerud, T. / De Fusco, C. / Brandt, P. / Bergstrom, F. / Johansson, P. / Ek, M. / Borjesson, U. / Johansson, A. / Danielsson, J. / Bauer, M. / Arnaud, B. / Castaldo, M. / Stromstedt, M. / ...Authors: Akerud, T. / De Fusco, C. / Brandt, P. / Bergstrom, F. / Johansson, P. / Ek, M. / Borjesson, U. / Johansson, A. / Danielsson, J. / Bauer, M. / Arnaud, B. / Castaldo, M. / Stromstedt, M. / Rosengren, B. / Jansen, F. / Fredlund, L.
History
DepositionSep 25, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide N-methyltransferase
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6086
Polymers62,4792
Non-polymers1,1294
Water6,900383
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8043
Polymers31,2401
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8043
Polymers31,2401
Non-polymers5652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.88, 69.71, 114.47
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 31239.545 Da / Num. of mol.: 2 / Mutation: K100A,E101A,E103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-A1IPM / 1,4-dimethyl-6-(methylamino)pyridine-3-carboxamide


Mass: 180.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 32% PEG3350, 0.2 M NaAc, and 0.1 M Hepes pH 6.8-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.67→44.2 Å / Num. obs: 57162 / % possible obs: 98.9 % / Redundancy: 6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.5
Reflection shellResolution: 1.67→1.73 Å / Num. unique obs: 4956 / CC1/2: 0.492

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→44.23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.107 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2837 -RANDOM
Rwork0.191 ---
obs0.193 57162 98.8 %-
Displacement parametersBiso mean: 31.09 Å2
Baniso -1Baniso -2Baniso -3
1-4.1242 Å20 Å20 Å2
2--5.3328 Å20 Å2
3----9.457 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.67→44.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 78 383 4427
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014160HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.045642HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1436SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes720HARMONIC5
X-RAY DIFFRACTIONt_it4160HARMONIC20
X-RAY DIFFRACTIONt_chiral_improper_torsion530SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5367SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.89
X-RAY DIFFRACTIONt_other_torsion16.24
LS refinement shellResolution: 1.67→1.69 Å
RfactorNum. reflection% reflection
Rfree0.2455 53 -
Rwork0.237 --
obs0.2374 1144 71.18 %

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