[English] 日本語
Yorodumi
- PDB-1e1y: Flavopiridol inhibits glycogen phosphorylase by binding at the in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e1y
TitleFlavopiridol inhibits glycogen phosphorylase by binding at the inhibitor site
ComponentsGLYCOGEN PHOSPHORYLASE, MUSCLE FORM
KeywordsTRANSFERASE / ALLOSTERIC INHIBITION
Function / homology
Function and homology information


glycogen phosphorylase / glycogen phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Glycosyl transferase, family 35 / Glycogen/starch/alpha-glucan phosphorylase / Phosphorylase pyridoxal-phosphate attachment site / Carbohydrate phosphorylase / Phosphorylase pyridoxal-phosphate attachment site. / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CPB / alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / PHOSPHITE ION / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsOikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Tsitsanou, K.E. / Johnson, L.N.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Flavopiridol Inhibits Glycogen Phosphorylase by Binding at the Inhibitor Site
Authors: Oikonomakos, N.G. / Schnier, J.B. / Zographos, S.E. / Skamnaki, V.T. / Tsitsanou, K.E. / Johnson, L.N.
#1: Journal: Protein Sci. / Year: 1999
Title: Allosteric Inhibition of Glycogen Phosphorylase a by the Potential Antidiabetic Drug 3-Isopropyl 4-(2-Chlorophenyl)-1,4-Dihydro-1-Ethyl-2-Methyl-Pyridine-3,5,6-Tricarboxylate
Authors: Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. / Goldmann, S. / Bischoff, H.
#2: Journal: Structure / Year: 1997
Title: The Structure of Glycogen Phosphorylase B with an Alkyl-Dihydropyridine-Dicarboxylic Acid Compound, a Novel and Potent Inhibitor
Authors: Zographos, S.E. / Oikonomakos, N.G. / Tsitsanou, K.E. / Leonidas, D.D. / Chrysina, E.D. / Skamnaki, V.T. / Bischoff, H. / Goldman, S. / Schramm, M. / Watson, K.A. / Johnson, L.N.
History
DepositionMay 11, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1995
Polymers97,2911
Non-polymers9084
Water11,602644
1
A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules

A: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,39910
Polymers194,5822
Non-polymers1,8168
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area9920 Å2
ΔGint-19.1 kcal/mol
Surface area56260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.759, 126.759, 116.018
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2024-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein GLYCOGEN PHOSPHORYLASE, MUSCLE FORM / MYOPHOSPHORYLASE


Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#4: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 4 types, 647 molecules

#2: Chemical ChemComp-CPB / 2-(2-CHLORO-PHENYL)-5,7-DIHYDROXY-8-(3-HYDROXY-1-METHYL-PIPERIDIN-4-YL)-4H-BENZOPYRAN-4-ONE / FLAVOPIRIDOL


Mass: 401.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20ClNO5
#3: Chemical ChemComp-PO3 / PHOSPHITE ION


Mass: 78.972 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO3
#5: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence details2AMV SWALL P00489 1 - 13 NOT IN ATOMS LI REFERENCE: K.NAKANO, P.K.HWANG, R.J.FLETTERICK, FEBS LETT. ...2AMV SWALL P00489 1 - 13 NOT IN ATOMS LI REFERENCE: K.NAKANO, P.K.HWANG, R.J.FLETTERICK, FEBS LETT., V. 204, P. 283, 1986. HIGH RESOLUTION DATA (1.5 ANGSTROMS) REFINEMENT ON T-STATE GLYCOGEN PHOSPHORYLASE (UNPUBLISHED RESULTS) HAS CONFIRMED THAT RESIDUE 609 IS INDEED ALA (NOT PRO).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.7
Details: AS DESCRIBED PREVIOUSLY BY OIKONOMAKOS ET AL. (1999) PROTEIN SCIENCE 8, 1930-1945., pH 6.70
Crystal grow
*PLUS
Method: co-crystallization
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mg/mlenzyme11
21 mMflavopiridol11
33 mMdithiothreitol11
410 mMBes11
50.1 mMEDTA11
60.02 %sodium azide11
71 mMspermine11or 10 mM magnesium acetate
850 mMglucose11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.05
DetectorDate: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.23→29.9 Å / Num. obs: 40691 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.1
Reflection shellResolution: 2.23→2.27 Å / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.4 / % possible all: 84.6
Reflection
*PLUS
Num. measured all: 321450
Reflection shell
*PLUS
% possible obs: 84.6 %

-
Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GPA

2gpa


Resolution: 2.23→29.9 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: RESIDUES WHERE OVERALL -FACTOR VALUES EXCEED 60 A**2 INCLUDE 16-22 (71.1), 550-556 (69.4), AND 837-838 (75.9). TER PRO: RESIDUES 1-5,251-259,315-324,839- 842 WERE NOT DEFINED BY ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.252 -5 %RANDOM
Rwork0.195 ---
obs0.195 40691 87.3 %-
Refinement stepCycle: LAST / Resolution: 2.23→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6617 0 59 644 7320
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.24
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_scangle_it2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65
LS refinement shell
*PLUS
Rfactor Rfree: 0.314 / Rfactor Rwork: 0.252

+
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