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- PDB-2ony: Structure of hPNMT with inhibitor 7-(N-4-chlorophenylaminosulfony... -

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Basic information

Entry
Database: PDB / ID: 2ony
TitleStructure of hPNMT with inhibitor 7-(N-4-chlorophenylaminosulfonyl)-THIQ and AdoHcy
ComponentsPhenylethanolamine N-methyltransferase
KeywordsTRANSFERASE / methyltransferase
Function / homology
Function and homology information


phenylethanolamine N-methyltransferase / phenylethanolamine N-methyltransferase activity / epinephrine biosynthetic process / Catecholamine biosynthesis / catecholamine biosynthetic process / 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. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Chem-TMJ / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsDrinkwater, N. / Martin, J.L.
CitationJournal: J.Med.Chem. / Year: 2007
Title: Enzyme Adaptation to Inhibitor Binding: A Cryptic Binding Site in Phenylethanolamine N-Methyltransferase
Authors: Gee, C.L. / Drinkwater, N. / Tyndall, J.D.A. / Grunewald, G.L. / Wu, Q. / McLeish, M.J. / Martin, J.L.
History
DepositionJan 24, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,8796
Polymers63,6922
Non-polymers1,1874
Water2,846158
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5533
Polymers31,8461
Non-polymers7072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3253
Polymers31,8461
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-23 kcal/mol
Surface area20170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.960, 93.960, 188.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Phenylethanolamine N-methyltransferase / PNMTase / Noradrenaline N-methyltransferase


Mass: 31845.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PNMT-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P11086, phenylethanolamine 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-TMJ / N-(4-CHLOROPHENYL)-1,2,3,4-TETRAHYDROISOQUINOLINE-7-SULFONAMIDE / 7-(N-4-CHLOROPHENYL-AMINSULFONYL)-1,2,3,4-TETRAHYDROISOQUINOLINE


Mass: 322.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15ClN2O2S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 8% PEG6K, 0.25M LiCl, 0.1M cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 7, 2006
RadiationMonochromator: MaxScreen / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→45.58 Å / Num. obs: 26667 / % possible obs: 99.9 % / Redundancy: 6.17 % / Rmerge(I) obs: 0.051 / Χ2: 0.98 / Net I/σ(I): 14.3 / Scaling rejects: 1245
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.6-2.696.20.4952.21645126231.46100
2.69-2.86.220.3882.91629225941.3499.9
2.8-2.936.230.3113.51649526231.28100
2.93-3.086.250.2294.51652326211.14100
3.08-3.286.250.1596.41659226331.03100
3.28-3.536.190.0999.81656226590.86100
3.53-3.886.160.06414.51639626520.7499.9
3.88-4.446.180.04221.11669126850.67100
4.44-5.66.20.03131.11690927140.6399.9
5.6-45.585.890.02145.61697328630.6899

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata processing
CNS1.1refinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1HNN

1hnn


Resolution: 2.6→45.58 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 549065.438 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1220 4.8 %RANDOM
Rwork0.223 ---
obs-25311 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.766 Å2 / ksol: 0.311 e/Å3
Displacement parametersBiso mean: 68.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.23 Å20 Å20 Å2
2--9.23 Å20 Å2
3----18.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.6→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 78 158 4335
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d121
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.408 206 5.2 %
Rwork0.37 3733 -
obs-3939 90.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2tmc_mod.paramtmc_mod.top
X-RAY DIFFRACTION3sah_mod.paramsah_mod.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5ion.paramion.top

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