[English] 日本語
Yorodumi
- PDB-3amv: ALLOSTERIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3amv
TitleALLOSTERIC INHIBITION OF GLYCOGEN PHOSPHORYLASE A BY A POTENTIAL ANTIDIABETIC DRUG
ComponentsPROTEIN (GLYCOGEN PHOSPHORYLASE)
KeywordsTRANSFERASE / DIABETES / GLYCOGEN METABOLISM / PHOSPHORYLASE A / INHIBITION / ALLOSTERIC SITE
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-BIN / alpha-D-glucopyranose / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.1 Å
AuthorsOikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T.
Citation
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-tricarbo xylate.
Authors: Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. / Goldmann, S. / Bischoff, H.
#1: Journal: To be Published
Title: Effects of Commonly Used Cryoprotectants on Glycogen Phosphorylase Activity and Structure
Authors: Tsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W.J.
#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
DepositionFeb 18, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Feb 26, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2975
Polymers97,3711
Non-polymers9264
Water13,565753
1
A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules

A: PROTEIN (GLYCOGEN PHOSPHORYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,59510
Polymers194,7422
Non-polymers1,8528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area10760 Å2
ΔGint-36 kcal/mol
Surface area55880 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.200, 127.200, 115.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein PROTEIN (GLYCOGEN PHOSPHORYLASE)


Mass: 97371.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase
#2: 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, 756 molecules

#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-BIN / 2,3-DICARBOXY-4-(2-CHLORO-PHENYL)-1-ETHYL-5-ISOPROPOXYCARBONYL-6-METHYL-PYRIDINIUM


Mass: 406.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21ClNO6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / 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: 2.41 Å3/Da / Density % sol: 48 %
Crystal growpH: 6.7
Details: 1 MM W1807 IN A MEDIUM CONSISTING OF 20-24 MG/ML ENZYME, 10 MM MAGNESIUM ACETATE, 3 MM DTT, 10 MM BES, 0.1 MM EDTA, AND 0.02% SODIUM AZIDE, PH 6.7 (22 DEG C).
Crystal grow
*PLUS
Temperature: 100 K / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMGlc11
21 mMW180711

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→13 Å / Num. obs: 51612 / % possible obs: 92.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 11.35
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.5 / % possible all: 87.3
Reflection
*PLUS
Num. measured all: 337366
Reflection shell
*PLUS
% possible obs: 87.3 %

-
Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.1→13 Å / Cross valid method: R FREE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 -5 %RANDOM
Rwork0.189 ---
obs-51612 92.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6611 0 61 753 7425
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Num. reflection obs: 48964 / Num. reflection Rfree: 2648
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.9 Å2

+
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