[English] 日本語
Yorodumi
- PDB-3oe4: Rat catechol O-methyltransferase in complex with a catechol-type,... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3oe4
TitleRat catechol O-methyltransferase in complex with a catechol-type, purine-containing bisubstrate inhibitor - humanized form
ComponentsCatechol O-methyltransferaseCatechol-O-methyltransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL MEMBRANE / MAGNESIUM / MEMBRANE / METAL-BINDING / PHOSPHOPROTEIN / S-ADENOSYL-L-METHIONINE / SIGNAL-ANCHOR / TRANSFERASE / TRANSMEMBRANE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / S-adenosylhomocysteine metabolic process ...Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / positive regulation of homocysteine metabolic process / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol-containing compound metabolic process / S-adenosylhomocysteine metabolic process / response to salt / catechol O-methyltransferase activity / renal sodium excretion / : / : / renin secretion into blood stream / catechol O-methyltransferase / developmental process / renal filtration / renal albumin absorption / dopamine secretion / S-adenosylmethionine metabolic process / negative regulation of dopamine metabolic process / habituation / artery development / catecholamine metabolic process / short-term memory / cellular response to phosphate starvation / cerebellar cortex morphogenesis / dopamine catabolic process / norepinephrine metabolic process / glomerulus development / fear response / multicellular organismal reproductive process / synaptic transmission, dopaminergic / response to angiotensin / cellular response to cocaine / estrogen metabolic process / response to food / exploration behavior / cholesterol efflux / response to temperature stimulus / response to pain / dopamine metabolic process / response to corticosterone / prostaglandin metabolic process / glycogen metabolic process / startle response / detection of temperature stimulus involved in sensory perception of pain / response to inorganic substance / behavioral fear response / multicellular organismal response to stress / response to amphetamine / response to organic substance / kidney development / learning / female pregnancy / response to cytokine / negative regulation of smooth muscle cell proliferation / multicellular organism growth / visual learning / response to organic cyclic compound / memory / response to toxic substance / cognition / regulation of blood pressure / response to wounding / response to estrogen / cell body / gene expression / methylation / postsynapse / postsynaptic membrane / response to oxidative stress / vesicle / response to lipopolysaccharide / dendritic spine / response to hypoxia / learning or memory / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / magnesium ion binding / membrane / cytosol
Similarity search - Function
Catechol O-methyltransferase, eukaryotic / O-methyltransferase / Class I-like SAM-dependent O-methyltransferase / SAM-dependent O-methyltransferase class I-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-610 / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsEhler, A. / Schlatter, D. / Stihle, M. / Benz, J. / Rudolph, M.G.
CitationJournal: Chemistry / Year: 2011
Title: Molecular Recognition at the Active Site of Catechol-O-methyltransferase (COMT): Adenine Replacements in Bisubstrate Inhibitors
Authors: Ellermann, M. / Paulini, R. / Jakob-Roetne, R. / Lerner, C. / Borroni, E. / Roth, D. / Ehler, A. / Schweizer, W.B. / Schlatter, D. / Rudolph, M.G. / Diederich, F.
History
DepositionAug 12, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2012Group: Structure summary
Revision 1.3Aug 15, 2012Group: Structure summary
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1773
Polymers24,6941
Non-polymers4832
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Catechol O-methyltransferase
hetero molecules

A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3546
Polymers49,3892
Non-polymers9654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_645y+1,x-1,-z1
Buried area4780 Å2
ΔGint-22 kcal/mol
Surface area18640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.739, 50.739, 167.926
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Catechol O-methyltransferase / Catechol-O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 1 / Fragment: SOLUBLE FORM, UNP RESIDUES 44-264 / Mutation: M91I, Y95C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: LIVER / Gene: Comt / Plasmid: PDS56/RBSII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P22734, catechol O-methyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-610 / N-[(E)-3-[(2R,3S,4R,5R)-3,4-dihydroxy-5-purin-9-yl-oxolan-2-yl]prop-2-enyl]-2,3-dihydroxy-5-nitro-benzamide


Mass: 458.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N6O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RAT COMT WAS HUMANIZED, AND RESIDUE 91 ILE AND 95 CYS ARE HUMAN SEQUENCE REFERING TO ISOFORM 2 ...THE RAT COMT WAS HUMANIZED, AND RESIDUE 91 ILE AND 95 CYS ARE HUMAN SEQUENCE REFERING TO ISOFORM 2 OF P21964 (COMT_HUMAN).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 17, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→43.94 Å / Num. obs: 42098 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.64 % / Net I/σ(I): 16.03
Reflection shellResolution: 1.49→1.59 Å / Redundancy: 9.58 % / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0081refinement
XDS(VERSION December 28data reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 1.49→42.51 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.231 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. C-terminal beta-strand is domain-swapped with symmetry mate; 2. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 2062 5 %RANDOM
Rwork0.17839 ---
obs0.17958 39116 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.656 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.49→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 34 160 1867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221777
X-RAY DIFFRACTIONr_bond_other_d0.0010.021176
X-RAY DIFFRACTIONr_angle_refined_deg1.8942.0052421
X-RAY DIFFRACTIONr_angle_other_deg1.03732893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8815222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40424.86876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55315314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.928159
X-RAY DIFFRACTIONr_chiral_restr0.1290.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211959
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02330
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 147 -
Rwork0.277 2688 -
obs--93.1 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more