[English] 日本語
Yorodumi
- PDB-1xc7: Binding of beta-D-glucopyranosyl bismethoxyphosphoramidate to gly... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xc7
TitleBinding of beta-D-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b: Kinetic and crystallographic studies
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE / glycogenolysis / type 2 diabetes
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-GL6 / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsChrysina, E.D. / Kosmopoulou, M.N. / Kardakaris, R. / Bischler, N. / Leonidas, D.D. / Kannan, T. / Loganathan, D. / Oikonomakos, N.G.
Citation
Journal: Bioorg.Med.Chem. / Year: 2005
Title: Binding of beta-d-glucopyranosyl bismethoxyphosphoramidate to glycogen phosphorylase b: kinetic and crystallographic studies
Authors: Chrysina, E.D. / Kosmopoulou, M.N. / Kardakaris, R. / Bischler, N. / Leonidas, D.D. / Kannan, T. / Loganathan, D. / Oikonomakos, N.G.
#1: Journal: BIOCATAL.BIOTRANSFOR. / Year: 2003
Title: Crystallographic studies on alpha and beta-D-glucopyranosyl formamide analogues, inhibitors of glycogen phosphorylase
Authors: Chrysina, E.D. / Oikonomakos, N.G. / Zographos, S.E. / Kosmopoulou, M.N. / Bischler, N. / Leonidas, D. / Kovacs, L. / Docsa, T. / Gergely, P. / Somsak, L.
#2: Journal: Eur.J.Biochem. / Year: 2002
Title: Binding of N-acetyl-N '-beta-D-glucopyranosyl urea and N-benzoyl-N '-beta-D-glucopyranosyl urea to glycogen phosphorylase b: kinetic and crystallographic studies
Authors: Oikonomakos, N.G. / Kosmopoulou, M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Somsak, L. / Nagy, V. / Praly, J.P. / Docsa, T. / Toth, B. / Gergely, P.
History
DepositionSep 1, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / 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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
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)97,9224
Polymers97,2911
Non-polymers6303
Water6,395355
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,8438
Polymers194,5822
Non-polymers1,2616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7080 Å2
ΔGint-43 kcal/mol
Surface area57330 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.733, 128.733, 116.229
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-1320-

HOH

21A-1345-

HOH

-
Components

#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: MuscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase
#2: Sugar ChemComp-GL6 / N-(dimethoxyphosphoryl)-beta-D-glucopyranosylamine


Type: D-saccharide / Mass: 287.204 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H18NO8P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.79 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 298 K / Method: small tubes / pH: 6.8 / Details: pH 6.8, SMALL TUBES, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 7, 2003 / Details: mirrors
RadiationMonochromator: Daresbury / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.83→30 Å / Num. all: 84865 / Num. obs: 84865 / % possible obs: 98.3 % / Observed criterion σ(F): 1.83 / Observed criterion σ(I): 1.83 / Redundancy: 7.3 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 13.2
Reflection shellResolution: 1.83→1.86 Å / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.7 / Num. unique all: 4137 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→29.36 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3256777.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.209 4305 5.1 %RANDOM
Rwork0.191 ---
obs0.191 84727 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.8336 Å2 / ksol: 0.332471 e/Å3
Displacement parametersBiso mean: 34.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.66 Å20 Å20 Å2
2--4.61 Å20 Å2
3----7.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.83→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 38 355 6976
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 729 5.3 %
Rwork0.251 13129 -
obs--97.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PLP.PARAMPLP.TOP
X-RAY DIFFRACTION4DL-1B_SMALL.PARAMDL-1B_SMALL.TOP
X-RAY DIFFRACTION5PARAM.SULPHATETOP.SULPHATE

+
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