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- PDB-2g70: Structure of human PNMT in complex with inhibitor 3-hydroxymethyl... -

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Basic information

Entry
Database: PDB / ID: 2g70
TitleStructure of human PNMT in complex with inhibitor 3-hydroxymethyl-7-nitro-THIQ and AdoMet (SAM)
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-HNT / PHOSPHATE ION / S-ADENOSYLMETHIONINE / Phenylethanolamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)65,2088
Polymers63,6922
Non-polymers1,5166
Water1,45981
1
A: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6614
Polymers31,8461
Non-polymers8153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phenylethanolamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5484
Polymers31,8461
Non-polymers7023
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 area2480 Å2
ΔGint-12 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.240, 94.240, 187.810
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) / 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


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-HNT / [(3R)-7-NITRO-1,2,3,4-TETRAHYDROISOQUINOLIN-3-YL]METHANOL / 3(R)-HYDROXYMETHYL 7-NITRO 1,2,3,4-TETRAHYDROISOQUINOLINE


Mass: 208.214 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12N2O3
#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.: 81 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.6M ammonium phosphate, 0.1M Sodium citrate, pH 5.3, 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: Jul 1, 2003
RadiationMonochromator: HiRes2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→29.8 Å / Num. obs: 33540 / % possible obs: 99 % / Redundancy: 7.07 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.074 / Χ2: 0.97 / Net I/σ(I): 12.7 / Scaling rejects: 1792
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 97.9 % / Redundancy: 7.25 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3.6 / Num. measured all: 23577 / Num. unique all: 3234 / Num. unique obs: 3249 / Χ2: 1.08 / % possible all: 97.9

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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: 2.4→29.8 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3338 9.9 %random
Rwork0.24 ---
all-33863 --
obs-33484 98.9 %-
Solvent computationBsol: 40.432 Å2
Displacement parametersBiso mean: 60.036 Å2
Baniso -1Baniso -2Baniso -3
1--6.772 Å20 Å20 Å2
2---6.772 Å20 Å2
3---13.544 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 104 81 4291
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_deg0.99
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.435 305 -
Rwork0.415 --
obs-3234 97.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2sam_mod3.param
X-RAY DIFFRACTION3hmn_cns.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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