[English] 日本語
Yorodumi
- PDB-4yi3: Crystal structure of Gpb in complex with 4a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yi3
TitleCrystal structure of Gpb in complex with 4a
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / alpha and beta protein
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-4D0 / INOSINIC ACID / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKantsadi, A.L. / Chatzileontiadou, D.S.M. / Stravodimos, G.A. / Leonidas, D.D.
Funding support Greece, 1items
OrganizationGrant numberCountry
ARISTEIA" Action of the "Operational Programme Education and Lifelong Learning1492 Greece
CitationJournal: Curr Top Med Chem / Year: 2015
Title: Glycogen phosphorylase as a target for type 2 diabetes: synthetic, biochemical, structural and computational evaluation of novel N-acyl-N -( beta-D-glucopyranosyl) urea inhibitors.
Authors: Kantsadi, A.L. / Parmenopoulou, V. / Bakalov, D.N. / Snelgrove, L. / Stravodimos, G.A. / Chatzileontiadou, D.S. / Manta, S. / Panagiotopoulou, A. / Hayes, J.M. / Komiotis, D. / Leonidas, D.D.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
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)98,5265
Polymers97,4221
Non-polymers1,1044
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-0 kcal/mol
Surface area30700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.460, 128.460, 116.580
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-1344-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P00489, glycogen phosphorylase

-
Non-polymers , 5 types, 350 molecules

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


Mass: 247.142 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H10NO6P
#3: Chemical ChemComp-4D0 / N-{[3-(biphenyl-4-yl)propanoyl]carbamoyl}-beta-D-glucopyranosylamine


Mass: 430.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N2O7
#4: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.15 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10mM BES buffer

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0403 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 3, 2014
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0403 Å / Relative weight: 1
ReflectionResolution: 1.8→38.36 Å / Num. all: 90140 / Num. obs: 6609 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rsym value: 0.078 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
SCALAdata scaling
DENZOdata reduction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MHO

4mho


Resolution: 1.8→38.36 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.348 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19762 4420 4.9 %RANDOM
Rwork0.1743 ---
obs0.17546 85720 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å2-0 Å2-0 Å2
2--0.76 Å2-0 Å2
3----1.52 Å2
Refinement stepCycle: 1 / Resolution: 1.8→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6556 0 73 346 6975
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196792
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.9639201
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5725807
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18323.526346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.482151170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2351559
X-RAY DIFFRACTIONr_chiral_restr0.0930.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215208
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.342.7133225
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.1864.0594027
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.0753.1053567
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.52123.51210333
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 303 -
Rwork0.256 6306 -
obs--99.91 %

+
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