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- PDB-2aou: Histamine Methyltransferase Complexed with the Antimalarial Drug ... -

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Basic information

Entry
Database: PDB / ID: 2aou
TitleHistamine Methyltransferase Complexed with the Antimalarial Drug Amodiaquine
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
Chem-CQA / Histamine N-methyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN Any one of the three ethyl groups on ligand, CQA 400 could be the alternative ...HETEROGEN Any one of the three ethyl groups on ligand, CQA 400 could be the alternative conformation of the other two (by the rotation of approximately 120 or 240 drgrees).

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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)68,1216
Polymers66,6982
Non-polymers1,4234
Water5,513306
1
A: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0613
Polymers33,3491
Non-polymers7122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histamine N-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0613
Polymers33,3491
Non-polymers7122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.890, 130.890, 63.320
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: 33349.020 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: 33349.020 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-CQA / 4-[(7-CHLOROQUINOLIN-4-YL)AMINO]-2-[(DIETHYLAMINO)METHYL]PHENOL / AMODIAQUINE / FLAVOQUINE


Mass: 355.861 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22ClN3O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 6000, MES, ethyleneglycol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jun 23, 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: 2.3→30 Å / Num. all: 27645 / Num. obs: 26928 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.35 Å / % possible all: 96.2

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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: 2.3→30 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 2696 -RANDOM
Rwork0.207 ---
all0.213 26928 --
obs0.213 26928 97.4 %-
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å21.65 Å20 Å2
2---1.33 Å20 Å2
3---2.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-30 Å
Luzzati sigma a0.26 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4515 0 96 306 4917
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.3→2.35 Å / Rfactor Rfree error: 0.024 /
RfactorNum. reflection
Rfree0.3 159
Rwork0.237 -
obs-1611

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