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- PDB-7wmc: Crystal structure of macrocyclic peptide 1 bound to human Nicotin... -

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Basic information

Entry
Database: PDB / ID: 7wmc
TitleCrystal structure of macrocyclic peptide 1 bound to human Nicotinamide N-methyltransferase
Components
  • Nicotinamide N-methyltransferase
  • Peptide1
KeywordsTRANSFERASE / Nicotinamide N-methyltransferase
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
Nicotinamide N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
unidentified (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsYoshida, S. / Uehara, S. / Kondo, N. / Takahashi, Y. / Yamamoto, S. / Kameda, A. / Kawagoe, S. / Inoue, N. / Yamada, M. / Yoshimura, N. / Tachibana, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Peptide-to-Small Molecule: A Pharmacophore-Guided Small Molecule Lead Generation Strategy from High-Affinity Macrocyclic Peptides.
Authors: Yoshida, S. / Uehara, S. / Kondo, N. / Takahashi, Y. / Yamamoto, S. / Kameda, A. / Kawagoe, S. / Inoue, N. / Yamada, M. / Yoshimura, N. / Tachibana, Y.
History
DepositionJan 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinamide N-methyltransferase
C: Peptide1
E: Peptide1
B: Nicotinamide N-methyltransferase
D: Peptide1


Theoretical massNumber of molelcules
Total (without water)61,4175
Polymers61,4175
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9060 Å2
ΔGint-54 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.021, 70.021, 227.598
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Nicotinamide N-methyltransferase


Mass: 28891.164 Da / Num. of mol.: 2
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 Peptide1


Mass: 1211.415 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others) / Production host: synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 15%(w/v)PEG3350, 0.1 M sodium malonate pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.55→75.87 Å / Num. obs: 22069 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.035 / Rrim(I) all: 0.12 / Χ2: 1.084 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.55-2.6410.80.49721690.9470.1550.5211.062
2.64-2.7510.80.40121380.960.1260.421.071
2.75-2.8710.70.30521660.9780.0960.321.127
2.87-3.0210.70.24821800.9820.0780.261.112
3.02-3.2110.70.19321610.9890.0610.2021.112
3.21-3.4610.90.13621820.9940.0430.1421.151
3.46-3.8111.10.10921990.9960.0340.1151.143
3.81-4.3611.50.08222240.9980.0250.0861.106
4.36-5.49120.06922460.9980.0210.0721.005
5.49-5012.40.05424040.9990.0160.0560.989

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.318
Highest resolutionLowest resolution
Rotation47.37 Å2.69 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
REFMAC5.8.0218refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→75.87 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.894 / SU B: 8.843 / SU ML: 0.193 / SU R Cruickshank DPI: 0.3982 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.398 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2555 1032 4.7 %RANDOM
Rwork0.1861 ---
obs0.1893 20981 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.26 Å2 / Biso mean: 32.468 Å2 / Biso min: 10.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 2.55→75.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3770 0 0 68 3838
Biso mean---26.37 -
Num. residues----485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193859
X-RAY DIFFRACTIONr_bond_other_d0.0010.023511
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9925224
X-RAY DIFFRACTIONr_angle_other_deg0.8623.0018140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9875476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71624.452155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63215623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0591515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
LS refinement shellResolution: 2.55→2.615 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.397 70 -
Rwork0.241 1513 -
obs--98.81 %

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