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- PDB-7ehz: Structure of human NNMT in complex with macrocyclic peptide 2 -

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Basic information

Entry
Database: PDB / ID: 7ehz
TitleStructure of human NNMT in complex with macrocyclic peptide 2
Components
  • Nicotinamide N-methyltransferase
  • macrocyclic peptide 2
KeywordsTRANSFERASE / Nicotinamide N-methyltransferase
Function / homology
Function and homology information


pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration ...pyridine N-methyltransferase activity / nicotinamide N-methyltransferase / nicotinamide metabolic process / nicotinamide N-methyltransferase activity / Metabolism of ingested SeMet, Sec, MeSec into H2Se / positive regulation of protein deacetylation / NAD biosynthesis via nicotinamide riboside salvage pathway / Methylation / Nicotinamide salvaging / animal organ regeneration / positive regulation of gluconeogenesis / response to organonitrogen compound / methylation / response to xenobiotic stimulus / 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
Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHayashi, K. / Mikamiyama, H. / Uehara, S. / Yamamoto, S. / Cary, D. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. ...Hayashi, K. / Mikamiyama, H. / Uehara, S. / Yamamoto, S. / Cary, D. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. / Kawai, T. / Ono, T. / Yamamoto, S. / Fumoto, M.
CitationJournal: Acs Med.Chem.Lett. / Year: 2021
Title: Macrocyclic Peptides as a Novel Class of NNMT Inhibitors: A SAR Study Aimed at Inhibitory Activity in the Cell.
Authors: Hayashi, K. / Uehara, S. / Yamamoto, S. / Cary, D.R. / Nishikawa, J. / Ueda, T. / Ozasa, H. / Mihara, K. / Yoshimura, N. / Kawai, T. / Ono, T. / Yamamoto, S. / Fumoto, M. / Mikamiyama, H.
History
DepositionMar 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide N-methyltransferase
B: macrocyclic peptide 2


Theoretical massNumber of molelcules
Total (without water)30,0952
Polymers30,0952
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-6 kcal/mol
Surface area11000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.081, 68.057, 45.205
Angle α, β, γ (deg.)90.000, 104.280, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 28891.164 Da / Num. of mol.: 1 / Mutation: E103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NNMT / Production host: Escherichia coli (E. coli)
References: UniProt: P40261, nicotinamide N-methyltransferase
#2: Protein/peptide macrocyclic peptide 2


Mass: 1203.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 42.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Bicine pH9.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 9031 / % possible obs: 99.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Rrim(I) all: 0.077 / Χ2: 1.041 / Net I/σ(I): 13.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.593.40.2748890.9380.1750.3271.01100
2.59-2.693.50.239070.9450.1440.2721.104100
2.69-2.823.60.1958920.9570.120.2290.977100
2.82-2.963.60.1588850.9730.0970.1861.022100
2.96-3.153.70.1249010.9820.0750.1450.978100
3.15-3.393.70.0959150.9860.0580.1111.045100
3.39-3.733.70.0749000.9920.0450.0871.018100
3.73-4.273.70.0629140.9940.0380.0721.08699.9
4.27-5.383.70.0498970.9960.030.0581.03199.9
5.38-503.60.0449310.9960.0270.0521.13699.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.525
Highest resolutionLowest resolution
Rotation42.2 Å2.75 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
MOLREP11.6.02phasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ROD

3rod


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.608 / SU ML: 0.259 / SU R Cruickshank DPI: 0.6682 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.668 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 454 5 %RANDOM
Rwork0.1933 ---
obs0.1966 8577 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.61 Å2 / Biso mean: 49.802 Å2 / Biso min: 29.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20.21 Å2
2---0.16 Å20 Å2
3---0.02 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 0 24 1890
Biso mean---47.66 -
Num. residues----245
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191911
X-RAY DIFFRACTIONr_angle_refined_deg1.772.0032597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7645240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97124.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.22915296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.797157
X-RAY DIFFRACTIONr_chiral_restr0.1150.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211438
LS refinement shellResolution: 2.5→2.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 30 -
Rwork0.257 558 -
all-588 -
obs--88.29 %

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