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- PDB-2g72: Structure of hPNMT with inhibitor 3-fluoromethyl-7-thiomorpholino... -

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Basic information

Entry
Database: PDB / ID: 2g72
TitleStructure of hPNMT with inhibitor 3-fluoromethyl-7-thiomorpholinosulfonamide-THIQ and AdoMet
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-F21 / S-ADENOSYLMETHIONINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsTyndall, J.D.A. / Gee, C.L. / 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
DepositionFeb 27, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2007Group: 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)65,1506
Polymers63,6922
Non-polymers1,4584
Water4,684260
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5753
Polymers31,8461
Non-polymers7292
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5753
Polymers31,8461
Non-polymers7292
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 area2470 Å2
ΔGint-11 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.310, 94.310, 188.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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) / Gene: pnmt / Plasmid: PNMT-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P11086, phenylethanolamine N-methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-F21 / (3R)-3-(FLUOROMETHYL)-7-(THIOMORPHOLIN-4-YLSULFONYL)-1,2,3,4-TETRAHYDROISOQUINOLINE / 3-FLUOROMETHYL 7-THIOMORPHOLINOSULFONAMIDE 1,2,3,4-TETRAHYDROISOQUINOLINE


Mass: 330.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H19FN2O2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 62.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: PEG6K, LiCl, cacodylate, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 5, 2004
RadiationMonochromator: HiRes2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→32.84 Å / Num. obs: 58197 / % possible obs: 99.8 % / Redundancy: 11.71 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.99 / Net I/σ(I): 17.5 / Scaling rejects: 5149
Reflection shellResolution: 2→2.07 Å / % possible obs: 99 % / Redundancy: 11.38 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 4.6 / Num. measured all: 64721 / Num. unique all: 5662 / Num. unique obs: 5662 / Χ2: 1.16 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata 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→31.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3067226.5 / 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
Rfree0.262 5908 10.2 %RANDOM
Rwork0.226 ---
all-58347 --
obs-58130 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.823 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1-5.22 Å20 Å20 Å2
2--5.22 Å20 Å2
3----10.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4137 0 96 260 4493
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_deg1.03
X-RAY DIFFRACTIONc_mcbond_it1.881.5
X-RAY DIFFRACTIONc_mcangle_it2.782
X-RAY DIFFRACTIONc_scbond_it3.082
X-RAY DIFFRACTIONc_scangle_it3.972.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.459 574 10.1 %
Rwork0.457 5085 -
obs-5659 98.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3far210b.paramfar210b.top
X-RAY DIFFRACTION4sam_mod4.paramsam_mod.top

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