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- PDB-9h5e: NNMT-SAH IN COMPLEX WITH 1p -

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Basic information

Entry
Database: PDB / ID: 9h5e
TitleNNMT-SAH IN COMPLEX WITH 1p
ComponentsNicotinamide N-methyltransferase
KeywordsTRANSFERASE / NNMT SAH SAM
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: 1.896 Å
AuthorsJohansson, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionOct 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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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
C: Nicotinamide N-methyltransferase
D: Nicotinamide N-methyltransferase
E: Nicotinamide N-methyltransferase
F: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,26918
Polymers187,9606
Non-polymers3,31012
Water12,070670
1
A: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8783
Polymers31,3271
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8783
Polymers31,3271
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8783
Polymers31,3271
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8783
Polymers31,3271
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8783
Polymers31,3271
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Nicotinamide N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8783
Polymers31,3271
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.59, 208, 114.77
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: 31326.623 Da / Num. of mol.: 6
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.: 6 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical
ChemComp-A1ISJ / 6-methoxy-1-methyl-pyridine-3-carboxamide


Mass: 167.185 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H11N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 670 / 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 % sol: 37.1 %
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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97995 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97995 Å / Relative weight: 1
ReflectionResolution: 1.9→48.1 Å / Num. obs: 116672 / % possible obs: 99.2 % / Redundancy: 6.5 % / CC1/2: 1 / Net I/σ(I): 5.5
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 1497 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (8-JUN-2022)refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.896→48.11 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.25 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.253 / SU Rfree Blow DPI: 0.206 / SU Rfree Cruickshank DPI: 0.206
RfactorNum. reflection% reflectionSelection details
Rfree0.3254 5834 -RANDOM
Rwork0.2935 ---
obs0.2951 116672 99.1 %-
Displacement parametersBiso mean: 40.54 Å2
Baniso -1Baniso -2Baniso -3
1-7.6409 Å20 Å20 Å2
2--5.3511 Å20 Å2
3----12.992 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 1.896→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12102 0 228 670 13000
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00812606HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9917082HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4362SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2124HARMONIC5
X-RAY DIFFRACTIONt_it12606HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1602SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11420SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion17.39
LS refinement shellResolution: 1.9→1.91 Å
RfactorNum. reflection% reflection
Rfree0.6078 117 -
Rwork0.5526 --
obs0.5552 2334 87.59 %
Refinement TLS params.

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)
10.78691.0268-0.02962.06930.08590.28280.17010.1249-0.0340.1249-0.213-0.0212-0.034-0.02120.0429-0.093-0.03550.0051-0.0830.0280.1957-3.087310.6248-15.2499
20.63920.2945-0.09341.1120.0090.59270.05510.03640.05170.0364-0.05580.00610.05170.00610.0007-0.0539-0.0004-0.0054-0.04390.01790.0571-27.2869-12.2972-15.2121
30.61-0.319-0.1710.9345-0.05360.68420.06-0.04270.0343-0.0427-0.04390.00640.03430.0064-0.0161-0.06120.0016-0.0144-0.0569-0.01660.1048-34.301922.3688-42.1783
40.7917-1.0227-0.02092.0976-0.09250.28720.1706-0.1254-0.0328-0.1254-0.21290.0248-0.03280.02480.0422-0.09430.0360.0051-0.0838-0.02880.19693.0872-24.0409-42.1356
50.6056-0.3466-0.15710.9826-0.03990.64170.0606-0.04090.0362-0.0409-0.04640.00380.03620.0038-0.0142-0.0590.0009-0.0136-0.0529-0.01520.0952-34.301-46.9643-42.1795
60.80961.034-0.02192.07560.09030.28920.16930.1248-0.03120.1248-0.2141-0.0224-0.0312-0.02240.0448-0.094-0.03580.0061-0.08460.02850.1977-3.087-58.7082-15.2477
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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