[English] 日本語
Yorodumi
- PDB-6qa8: Glycogen Phosphorylase b in complex with 28 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qa8
TitleGlycogen Phosphorylase b in complex with 28
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
Function / homology
Function and homology information


glycogen phosphorylase activity / SHG alpha-glucan phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / glycogen phosphorylase / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding
Similarity search - Function
Phosphorylase pyridoxal-phosphate attachment site / Glycogen/starch/alpha-glucan phosphorylase / Glycosyl transferase, family 35 / Phosphorylase pyridoxal-phosphate attachment site. / Carbohydrate phosphorylase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HTE / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsKyriakis, E. / Stravodimos, G.A. / Skamnaki, V.T. / Leonidas, D.D.
CitationJournal: J.Med.Chem. / Year: 2019
Title: Glucopyranosylidene-spiro-imidazolinones, a New Ring System: Synthesis and Evaluation as Glycogen Phosphorylase Inhibitors by Enzyme Kinetics and X-ray Crystallography.
Authors: Szabo, K.E. / Kyriakis, E. / Psarra, A.G. / Karra, A.G. / Sipos, A. / Docsa, T. / Stravodimos, G.A. / Katsidou, E. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Mandi, A. / Kiraly, S. ...Authors: Szabo, K.E. / Kyriakis, E. / Psarra, A.G. / Karra, A.G. / Sipos, A. / Docsa, T. / Stravodimos, G.A. / Katsidou, E. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Mandi, A. / Kiraly, S.B. / Kurtan, T. / Leonidas, D.D. / Somsak, L.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
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)97,9783
Polymers97,4221
Non-polymers5552
Water3,981221
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,9566
Polymers194,8452
Non-polymers1,1114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5380 Å2
ΔGint-19 kcal/mol
Surface area57120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.233, 128.233, 116.089
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#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: MuscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-HTE / (5~{S},7~{R},8~{S},9~{S},10~{R})-7-(hydroxymethyl)-8,9,10-tris(oxidanyl)-2-phenyl-6-oxa-1,3-diazaspiro[4.5]dec-1-en-4-one


Mass: 308.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O6
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7 / Details: 10 mM BES buffer

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5419 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.35→13.44 Å / Num. obs: 37248 / % possible obs: 91.6 % / Redundancy: 4.6 % / CC1/2: 0.993 / Rsym value: 0.073 / Net I/σ(I): 12.4
Reflection shellResolution: 2.35→2.44 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3258 / CC1/2: 0.804 / Rsym value: 0.61 / % possible all: 77.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
CrysalisProdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→13.44 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.935 / SU B: 14.698 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.356 / ESU R Free: 0.229 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21155 1826 4.9 %RANDOM
Rwork0.15725 ---
obs0.15989 35351 90.94 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 32.242 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å2-0 Å2
2--0.2 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.35→13.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6555 0 37 221 6813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0146741
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176015
X-RAY DIFFRACTIONr_angle_refined_deg1.1281.669128
X-RAY DIFFRACTIONr_angle_other_deg0.8491.63314088
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6425803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83321.559404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.528151168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2111559
X-RAY DIFFRACTIONr_chiral_restr0.0560.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027606
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021273
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_it2.6211.8883221
X-RAY DIFFRACTIONr_mcbond_other2.6211.8873220
X-RAY DIFFRACTIONr_mcangle_it3.7332.834021
X-RAY DIFFRACTIONr_mcangle_other3.7332.8314022
X-RAY DIFFRACTIONr_scbond_it4.5372.43520
X-RAY DIFFRACTIONr_scbond_other4.5372.3993521
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6983.4025108
X-RAY DIFFRACTIONr_long_range_B_refined7.522.3777590
X-RAY DIFFRACTIONr_long_range_B_other7.49822.3167566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 97 -
Rwork0.253 2168 -
obs--76.24 %
Refinement TLS params.Method: refined / Origin x: 28.115 Å / Origin y: 21.22 Å / Origin z: 31.358 Å
111213212223313233
T0.0402 Å2-0.0398 Å20.0023 Å2-0.0785 Å2-0.0245 Å2--0.0158 Å2
L0.6431 °20.0196 °20.0194 °2-0.5038 °2-0.1716 °2--0.9608 °2
S-0.0456 Å °0.0244 Å °0.0379 Å °-0.0017 Å °0.0159 Å °0.0201 Å °0.0629 Å °-0.1165 Å °0.0297 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