[English] 日本語
Yorodumi
- PDB-1ftw: STRUCTURES OF GLYCOGEN PHOSPHORYLASE-INHIBITOR COMPLEXES AND THE ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ftw
TitleSTRUCTURES OF GLYCOGEN PHOSPHORYLASE-INHIBITOR COMPLEXES AND THE IMPLICATIONS FOR STRUCTURE-BASED DRUG DESIGN
ComponentsGLYCOGEN PHOSPHORYLASE
KeywordsTRANSFERASE / GLYCOGEN PHOSPHORYLASE / INHIBITOR COMPLEX / CATALYTIC SITE / DESIGN
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-GL5 / PYRIDOXAL-5'-PHOSPHATE / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.36 Å
AuthorsWatson, K.A. / Tsitsanou, K.E. / Gregoriou, M. / Zographos, S.E. / Skamnaki, V.T. / Oikonomakos, N.G. / Fleet, G.W. / Johnson, L.N.
Citation
Journal: Proteins / Year: 2005
Title: Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase.
Authors: Watson, K.A. / Chrysina, E.D. / Tsitsanou, K.E. / Zographos, S.E. / Archontis, G. / Fleet, G.W. / Oikonomakos, N.G.
#1: Journal: Protein Sci. / Year: 1998
Title: The Structure of a Glycogen Phosphorylase Glucopyranose Spirohydantoin Complex at 1.8 A Resolution and 100K: The Role of the Water Structure and its Contribution to Binding
Authors: Gregoriou, M. / Noble, M.E. / Watson, K.A. / Garman, E.F. / Krulle, T.M. / de la Fuente, C. / Fleet, G.W. / Oikonomakos, N.G. / Johnson, L.N.
#2: Journal: Tetrahedron Lett. / Year: 1995
Title: Potent Inhibition of Glycogen Phosphorylase by a Spirohydantoin of Glucopyranose: First Pyranose Analogues of Hydantocidin
Authors: Bichard, C.J.F. / Mitchell, E.P. / Wormald, M.R. / Watson, K.A. / Johnson, L.N. / Zographos, S.E. / Koutra, D.D. / Oikonomakos, N.G. / Fleet, G.W.J.
#3: Journal: Protein Sci. / Year: 1995
Title: N-Acetyl-Beta-D-Glucopyranosylamine: A Potent T-State Inhibitor of Glycogen Phosphorylase. A Comparison with Alpha-D-Glucose
Authors: Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J. / Fleet, G.W. / Acharya, K.R.
#4: Journal: Biochemistry / Year: 1994
Title: Design of Inhibitors of Glycogen Phosphorylase: A Study of Alpha- and Beta-C-Glucosides and 1-Thio-Beta-D-Glucose Compounds
Authors: Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Son, J.C. / Bichard, C.J. / Orchard, M.G. / Fleet, G.W. / Oikonomakos, N.G. / Leonidas, D.D. / Kontou, M. / Papageorgiou, A.C.
History
DepositionSep 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8033
Polymers97,2911
Non-polymers5112
Water3,315184
1
A: GLYCOGEN PHOSPHORYLASE
hetero molecules

A: GLYCOGEN PHOSPHORYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,6056
Polymers194,5822
Non-polymers1,0234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7290 Å2
ΔGint-20 kcal/mol
Surface area58870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)128.500, 128.500, 116.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein GLYCOGEN PHOSPHORYLASE


Mass: 97291.203 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-GL5 / (5S,7R,8S,9S,10R)-3,8,9,10-tetrahydroxy-7-(hydroxymethyl)-6-oxa-1,3-diazaspiro[4.5]decane-2,4-dione / 3,8,9,10-TETRAHYDROXY-7-HYDROXYMETHYL-6-OXA-1,3-DIAZA-SPIRO[4.5]DECANE-2,4-DIONE


Type: D-saccharide / Mass: 264.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H12N2O8
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.47 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 289 K / Method: small tubes / pH: 6.7
Details: 10 mM BES, 0.1 MM EDTA, 1 mM IMP, 1 mM spermine , pH 6.70, SMALL TUBES, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6.7 / Method: unknown
Details: Oikonomakos, N.G., (1985) Biochim.Biophys.Acta., 832, 248.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
127.5 mg/mlphosphorylase b11
21.1 mMIMP11
31.1 mMspermine11
410 mMBes11
52.9 mMdithiothreitol11
60.1 mMEDTA11

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceType: OTHER / Wavelength: 1.5418
DetectorType: NICOLET IPC / Detector: AREA DETECTOR / Date: Mar 29, 1996
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.36→15.5 Å / Num. obs: 32684 / % possible obs: 81 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.36→2.47 Å
Reflection
*PLUS
Highest resolution: 2.36 Å / % possible obs: 81 % / Num. measured all: 145220 / Rmerge(I) obs: 0.08

-
Processing

Software
NameVersionClassification
CCP4model building
X-PLOR3.851refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER
Starting model: 2PRJ

2prj


Resolution: 2.36→15.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1598 5 %RANDOM
Rwork0.174 ---
obs-31501 81 %-
Refinement stepCycle: LAST / Resolution: 2.36→15.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6749 0 33 184 6966
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_deg1.4
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15.5 Å / % reflection Rfree: 5 % / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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