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- PDB-2aot: Histamine Methyltransferase Complexed with the Antihistamine Drug... -

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Basic information

Entry
Database: PDB / ID: 2aot
TitleHistamine Methyltransferase Complexed with the Antihistamine Drug Diphenhydramine
Components(Histamine N-methyltransferase) x 2
KeywordsTRANSFERASE / CLASSIC METHYLTRANSFERASE FOLD / PROTEIN-DRUG COMPLEX
Function / homology
Function and homology information


histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome ...histamine N-methyltransferase / histamine catabolic process / histamine N-methyltransferase activity / histamine metabolic process / Histidine catabolism / L-histidine catabolic process / Metabolism of ingested SeMet, Sec, MeSec into H2Se / respiratory gaseous exchange by respiratory system / methylation / centrosome / extracellular exosome / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Histamine N-methyltransferase-like / Histamine N-methyltransferase (EC 2.1.1.8) family profile. / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-[2-(BENZHYDRYLOXY)ETHYL]-N,N-DIMETHYLAMINE / S-ADENOSYL-L-HOMOCYSTEINE / Histamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHorton, J.R. / Sawada, K. / Nishibori, M. / Cheng, X.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: Structural basis for inhibition of histamine N-methyltransferase by diverse drugs
Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Cheng, X.
#1: Journal: Structure / Year: 2001
Title: Polymorphic Forms of Human Histamine Methyltransferase: Structural, Thermal, and Kinetic Comparisons
Authors: Horton, J.R. / Sawada, K. / Nishibori, M. / Zhang, X. / Cheng, X.
History
DepositionAug 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 9, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,0106
Polymers66,7302
Non-polymers1,2804
Water6,071337
1
A: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0053
Polymers33,3651
Non-polymers6402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0053
Polymers33,3651
Non-polymers6402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.67, 131.67, 63.75
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6

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Components

#1: Protein Histamine N-methyltransferase / HMT


Mass: 33365.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNMT / Plasmid: PGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P50135, histamine N-methyltransferase
#2: Protein Histamine N-methyltransferase


Mass: 33365.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNMT / Plasmid: PGEX-4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P50135
#3: Chemical ChemComp-2PM / N-[2-(BENZHYDRYLOXY)ETHYL]-N,N-DIMETHYLAMINE / DIPHENHYDRAMINE / ANTISTOMINUM / BENZHYDRAMINE


Mass: 255.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21NO
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, MES, ethyleneglycol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2000
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. all: 47507 / Num. obs: 47507 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.8
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.25 / Num. unique all: 2923 / % possible all: 95.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1JQD

1jqd


Resolution: 1.9→35 Å / Isotropic thermal model: ANISOTROPHIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.256 4792 RANDOM
Rwork0.221 --
all0.225 47507 -
obs0.225 47506 -
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å21.23 Å20 Å2
2--0.57 Å20 Å2
3---1.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-35 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4504 0 90 337 4931
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.031
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.1
LS refinement shellResolution: 1.9→1.94 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection
Rfree0.282 291
Rwork0.255 -
obs-2847

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