[English] 日本語
Yorodumi
- PDB-2gm9: Structure of rabbit muscle glycogen phosphorylase in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gm9
TitleStructure of rabbit muscle glycogen phosphorylase in complex with thienopyrrole
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE
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-3TH / Chem-PLR / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsOtterbein, L.R. / Pannifer, A.D. / Tucker, J. / Breed, J. / Oikonomakos, N.G. / Minshull, C. / Rowsell, S. / Pauptit, R.A.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: Novel thienopyrrole glycogen phosphorylase inhibitors: synthesis, in vitro SAR and crystallographic studies.
Authors: Whittamore, P.R. / Addie, M.S. / Bennett, S.N. / Birch, A.M. / Butters, M. / Godfrey, L. / Kenny, P.W. / Morley, A.D. / Murray, P.M. / Oikonomakos, N.G. / Otterbein, L.R. / Pannifer, A.D. / ...Authors: Whittamore, P.R. / Addie, M.S. / Bennett, S.N. / Birch, A.M. / Butters, M. / Godfrey, L. / Kenny, P.W. / Morley, A.D. / Murray, P.M. / Oikonomakos, N.G. / Otterbein, L.R. / Pannifer, A.D. / Parker, J.S. / Readman, K. / Siedlecki, P.S. / Schofield, P. / Stocker, A. / Taylor, M.J. / Townsend, L.A. / Whalley, D.P. / Whitehouse, J.
History
DepositionApr 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
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)95,8603
Polymers95,2811
Non-polymers5792
Water8,197455
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,7206
Polymers190,5622
Non-polymers1,1584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6950 Å2
ΔGint-42 kcal/mol
Surface area55740 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.781, 126.781, 115.144
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-1354-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis:

-
Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 95280.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Rabbit muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Chemical ChemComp-3TH / 2-CHLORO-N-[(3R)-2-OXO-1,2,3,4-TETRAHYDROQUINOLIN-3-YL]-6H-THIENO[2,3-B]PYRROLE-5-CARBOXAMIDE


Mass: 345.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12ClN3O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.1mM IMP 1.1mM Spermin 10mM BES 2.9mM DTT 0.1mM EDTA, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 7, 2001 / Details: Toroidal Zerodur mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.3→91.29 Å / Num. all: 40113 / Num. obs: 39447 / % possible obs: 98.34 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.54 Å / % possible all: 39.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IN HOUSE MODEL

Resolution: 2.3→91.29 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.894 / SU B: 15.732 / SU ML: 0.175 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1 / ESU R: 0.34 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 2093 5 %RANDOM
Rwork0.18249 ---
all0.18564 40113 --
obs0.18564 39447 98.34 %-
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: 29.819 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2--1.3 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6545 0 38 455 7038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226746
X-RAY DIFFRACTIONr_bond_other_d0.0020.026133
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9579132
X-RAY DIFFRACTIONr_angle_other_deg1.14314206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7845802
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3923.516347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.051151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1331560
X-RAY DIFFRACTIONr_chiral_restr0.090.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021442
X-RAY DIFFRACTIONr_nbd_refined0.2110.21556
X-RAY DIFFRACTIONr_nbd_other0.190.26516
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23197
X-RAY DIFFRACTIONr_nbtor_other0.0890.23925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2424
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.214
X-RAY DIFFRACTIONr_mcbond_it0.9571.55229
X-RAY DIFFRACTIONr_mcbond_other0.1651.51627
X-RAY DIFFRACTIONr_mcangle_it1.14126472
X-RAY DIFFRACTIONr_scbond_it1.88933207
X-RAY DIFFRACTIONr_scangle_it2.7544.52660
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 141 -
Rwork0.194 2719 -
obs--93.22 %
Refinement TLS params.Method: refined / Origin x: 21.1269 Å / Origin y: 98.8218 Å / Origin z: 2.3186 Å
111213212223313233
T-0.0336 Å20.0763 Å2-0.0144 Å2--0.0414 Å2-0.0115 Å2---0.0234 Å2
L0.0962 °2-0.0232 °2-0.0541 °2-0.2002 °2-0.0144 °2--0.4874 °2
S-0.0087 Å °0.0156 Å °-0.0115 Å °-0.0194 Å °-0.0226 Å °0.0025 Å °-0.0263 Å °-0.0574 Å °0.0314 Å °

+
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