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- PDB-2g8n: Structure of hPNMT with inhibitor 3-Hydroxymethyl-7-(N-4-chloroph... -

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Basic information

Entry
Database: PDB / ID: 2g8n
TitleStructure of hPNMT with inhibitor 3-Hydroxymethyl-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
Chem-F83 / S-ADENOSYL-L-HOMOCYSTEINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsDrinkwater, N. / Gee, C.L. / Martin, J.L.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Comparison of the Binding of 3-Fluoromethyl-7-sulfonyl-1,2,3,4-tetrahydroisoquinolines with Their Isosteric Sulfonamides to the Active Site of Phenylethanolamine N-Methyltransferase
Authors: Grunewald, G.L. / Seim, M.R. / Regier, R.C. / Martin, J.L. / Gee, C.L. / Drinkwater, N. / Criscione, K.R.
History
DepositionMar 2, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 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

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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)65,1666
Polymers63,6922
Non-polymers1,4744
Water5,278293
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5833
Polymers31,8461
Non-polymers7372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5833
Polymers31,8461
Non-polymers7372
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 area2540 Å2
ΔGint-18 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.320, 94.320, 188.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsthe biological unit is a monomer

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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-F83 / (3R)-N-(4-CHLOROPHENYL)-3-(HYDROXYMETHYL)-1,2,3,4-TETRAHYDROISOQUINOLINE-7-SULFONAMIDE / 3-HYDROXYMETHYL-7-(N-4-CHLOROPHENYLAMINOSULFONYL)-1,2,3,4-TETRAHYDROISOQUINOLINE


Mass: 352.836 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17ClN2O3S
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG6K, LiCl, cacodylate, pH 5.8, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 30, 2005
RadiationMonochromator: HiRes2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→45.78 Å / Num. obs: 47217 / % possible obs: 99.9 % / Redundancy: 7.76 % / Rmerge(I) obs: 0.049 / Χ2: 1.01 / Net I/σ(I): 16.7 / Scaling rejects: 2769
Reflection shellResolution: 2.15→2.23 Å / % possible obs: 99.7 % / Redundancy: 7.69 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 4.8 / Num. measured all: 35700 / Num. unique all: 7683 / Num. unique obs: 4622 / Χ2: 1.25 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata processing
CNS1.1refinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1HNN

1hnn


Resolution: 2.15→45.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2524808.75 / 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
Rfree0.243 4737 10.1 %RANDOM
Rwork0.201 ---
all-47165 --
obs-47132 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.356 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1-5.44 Å20 Å20 Å2
2--5.44 Å20 Å2
3----10.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.15→45.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 98 293 4497
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it3.21.5
X-RAY DIFFRACTIONc_mcangle_it4.192
X-RAY DIFFRACTIONc_scbond_it4.822
X-RAY DIFFRACTIONc_scangle_it5.792.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 761 9.9 %
Rwork0.278 6922 -
obs-7683 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION283_mod.paramwater.top
X-RAY DIFFRACTION3sah_mod2.paramsah_mod.top
X-RAY DIFFRACTION4water_rep.param83_mod.top

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