[English] 日本語
Yorodumi
- PDB-4pyq: Humanized rat apo-COMT in complex with a ureido-benzamidine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pyq
TitleHumanized rat apo-COMT in complex with a ureido-benzamidine
ComponentsCatechol O-methyltransferase
KeywordsTransferase/transferase inhibitor / METHYLTRANSFERASE / NEUROTRANSMITTER DEGRADATION / ALTERNATIVE INITIATION / CATECHOLAMINE METABOLISM / CELL MEMBRANE / MAGNESIUM / MEMBRANE / METAL-BINDING / PHOSPHOPROTEIN / SIGNAL-ANCHOR / TRANSMEMBRANE ANCHOR / ENZYME MECHANISM / CONFORMATIONAL CHANGE / Transferase-transferase inhibitor complex
Function / homology
Function and homology information


: / response to olanzapine / response to risperidone / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process ...: / response to olanzapine / response to risperidone / Enzymatic degradation of dopamine by COMT / Enzymatic degradation of Dopamine by monoamine oxidase / Methylation / norepinephrine secretion / response to dopamine / mastication / catecholamine catabolic process / catechol O-methyltransferase activity / S-adenosylhomocysteine metabolic process / catechol O-methyltransferase / developmental process / renal sodium excretion / renal filtration / S-adenosylmethionine metabolic process / renin secretion into blood stream / catecholamine metabolic process / dopamine secretion / renal albumin absorption / habituation / artery development / cerebellar cortex morphogenesis / dopamine catabolic process / response to salt / glomerulus development / norepinephrine metabolic process / response to angiotensin / fear response / short-term memory / synaptic transmission, dopaminergic / cellular response to phosphate starvation / cellular response to cocaine / estrogen metabolic process / cholesterol efflux / prostaglandin metabolic process / response to pain / response to food / response to corticosterone / response to temperature stimulus / negative regulation of dopamine metabolic process / glycogen metabolic process / response to stress / startle response / exploration behavior / dopamine metabolic process / detection of temperature stimulus involved in sensory perception of pain / behavioral fear response / multicellular organismal response to stress / response to cytokine / response to amphetamine / learning / kidney development / negative regulation of smooth muscle cell proliferation / female pregnancy / visual learning / response to wounding / response to toxic substance / regulation of blood pressure / response to estrogen / cognition / memory / multicellular organism growth / cell body / response to oxidative stress / response to lipopolysaccharide / methylation / gene expression / vesicle / dendritic spine / postsynaptic membrane / learning or memory / response to hypoxia / postsynapse / response to xenobiotic stimulus / axon / dendrite / glutamatergic synapse / magnesium ion binding / membrane / cytosol
Similarity search - Function
Catechol O-methyltransferase, eukaryotic / Class I-like SAM-dependent O-methyltransferase / 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-2X1 / ACETATE ION / Catechol O-methyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsEhler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Mapping the conformational space accessible to catechol-O-methyltransferase.
Authors: Ehler, A. / Benz, J. / Schlatter, D. / Rudolph, M.G.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2014Group: Database references
Revision 1.2Feb 28, 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_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catechol O-methyltransferase
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,53913
Polymers49,3892
Non-polymers1,15011
Water3,729207
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-104 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.366, 125.366, 77.287
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Catechol O-methyltransferase


Mass: 24694.332 Da / Num. of mol.: 2 / Fragment: unp residues 44-264 / Mutation: M134I, Y138C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Comt / Production host: Escherichia coli (E. coli) / References: UniProt: P22734, catechol O-methyltransferase

-
Non-polymers , 6 types, 218 molecules

#2: Chemical ChemComp-2X1 / 4-({[3-(aminomethyl)phenyl]carbamoyl}amino)benzenecarboximidamide


Mass: 283.328 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H17N5O
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.03 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: K,H,-L / Fraction: 0.5
ReflectionResolution: 1.39→36.4 Å / Num. obs: 91065 / % possible obs: 99.7 %
Reflection shellResolution: 1.39→1.44 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 1.491 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: dev_1589)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→36.41 Å / σ(F): 1.96 / Phase error: 17.87 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.161 4574 5.02 %
Rwork0.132 --
obs0.143 91056 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→36.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 73 207 3626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143521
X-RAY DIFFRACTIONf_angle_d1.3334782
X-RAY DIFFRACTIONf_dihedral_angle_d15.3451335
X-RAY DIFFRACTIONf_chiral_restr0.068533
X-RAY DIFFRACTIONf_plane_restr0.006613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3892-1.41310.35922200.34364288X-RAY DIFFRACTION94
1.4131-1.43880.33012120.31184324X-RAY DIFFRACTION95
1.4388-1.46650.28632310.26554320X-RAY DIFFRACTION95
1.4665-1.49640.29281980.25074386X-RAY DIFFRACTION96
1.4964-1.5290.2532460.21814364X-RAY DIFFRACTION95
1.529-1.56460.20532220.21094333X-RAY DIFFRACTION95
1.5646-1.60370.23572430.20124304X-RAY DIFFRACTION95
1.6037-1.6470.21272490.19084339X-RAY DIFFRACTION95
1.647-1.69550.20612300.18484334X-RAY DIFFRACTION95
1.6955-1.75020.19642380.17684326X-RAY DIFFRACTION95
1.7502-1.81280.18242610.1724287X-RAY DIFFRACTION94
1.8128-1.88540.18072240.16754330X-RAY DIFFRACTION95
1.8854-1.97120.18072180.16764350X-RAY DIFFRACTION95
1.9712-2.07510.20062330.16024327X-RAY DIFFRACTION95
2.0751-2.20510.18412310.15364277X-RAY DIFFRACTION94
2.2051-2.37530.17392140.14054322X-RAY DIFFRACTION95
2.3753-2.61430.16032180.13364306X-RAY DIFFRACTION94
2.6143-2.99240.162020.12244349X-RAY DIFFRACTION95
2.9924-3.76950.1362300.10014285X-RAY DIFFRACTION94
3.7695-36.41860.12972400.09274338X-RAY DIFFRACTION95

+
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