[English] 日本語
Yorodumi
- PDB-9frm: The crystal structure of glycogen phosphorylase with an indole de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9frm
TitleThe crystal structure of glycogen phosphorylase with an indole derivative
ComponentsGlycogen phosphorylase, muscle form
KeywordsTRANSFERASE
Function / homology
Function and homology information


maltodextrin phosphorylase activity / 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.
Similarity search - Domain/homology
: / Glycogen phosphorylase, muscle form
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKoulas, S.M. / Leonidas, D.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Med.Chem.Res. / Year: 2025
Title: Synthesis and evaluation of tetrahydrobenzo[cd]indole derivatives as glycogen phosphorylase inhibitors
Authors: Arunrattiyakorn, P. / Juiprasert, C. / Koulas, S.M. / Boonsri, P. / Aree, T. / Yagi-Utsumi, M. / Kato, K. / Leonidas, D.D.
History
DepositionJun 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

-
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)99,45519
Polymers97,6831
Non-polymers1,77318
Water9,854547
1
A: Glycogen phosphorylase, muscle form
hetero molecules

A: Glycogen phosphorylase, muscle form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,91138
Polymers195,3652
Non-polymers3,54536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)125.962, 125.962, 114.924
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Components on special symmetry positions
IDModelComponents
11A-901-

A1IFQ

21A-901-

A1IFQ

31A-1379-

HOH

41A-1509-

HOH

51A-1511-

HOH

-
Components

#1: Protein Glycogen phosphorylase, muscle form / Myophosphorylase


Mass: 97682.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase
#2: Chemical ChemComp-A1IFQ / (7~{S})-1-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)amino]-6,6-dimethyl-7-oxidanyl-7,8-dihydrobenzo[cd]indole-3-carboxylic acid


Mass: 444.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H24N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 289 K / Method: batch mode / pH: 6.7 / Details: 10 mM BES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.7293 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7293 Å / Relative weight: 1
ReflectionResolution: 2→44.53 Å / Num. obs: 62773 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 30.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.2
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 2798 / CC1/2: 0.885 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.53 Å / SU ML: 0.2083 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2155 3138 5 %RANDOM
Rwork0.1776 59635 --
obs0.1795 62773 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.44 Å2
Refinement stepCycle: LAST / Resolution: 2→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6552 0 116 547 7215
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076832
X-RAY DIFFRACTIONf_angle_d1.49219241
X-RAY DIFFRACTIONf_chiral_restr0.0519986
X-RAY DIFFRACTIONf_plane_restr0.00831210
X-RAY DIFFRACTIONf_dihedral_angle_d16.20012539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.31251390.23482659X-RAY DIFFRACTION99.96
2.03-2.060.25691350.20412669X-RAY DIFFRACTION100
2.06-2.10.22811480.19872685X-RAY DIFFRACTION100
2.1-2.140.271380.19392655X-RAY DIFFRACTION99.93
2.14-2.180.21831440.18842678X-RAY DIFFRACTION100
2.18-2.220.24971130.18412680X-RAY DIFFRACTION100
2.22-2.270.27251320.18542713X-RAY DIFFRACTION99.96
2.27-2.330.25581450.18252663X-RAY DIFFRACTION99.93
2.33-2.380.21061330.18162704X-RAY DIFFRACTION99.96
2.38-2.450.23641390.18222672X-RAY DIFFRACTION99.93
2.45-2.520.20971590.18552690X-RAY DIFFRACTION100
2.52-2.60.2471270.18982690X-RAY DIFFRACTION100
2.6-2.690.25231450.19442705X-RAY DIFFRACTION99.96
2.69-2.80.19891450.19942702X-RAY DIFFRACTION99.96
2.8-2.930.2481450.19332710X-RAY DIFFRACTION100
2.93-3.080.23051480.19152697X-RAY DIFFRACTION100
3.08-3.280.2341510.1872717X-RAY DIFFRACTION100
3.28-3.530.20611430.1742727X-RAY DIFFRACTION100
3.53-3.880.20011550.16272735X-RAY DIFFRACTION100
3.89-4.450.19141480.14722764X-RAY DIFFRACTION100
4.45-5.60.1771670.15632786X-RAY DIFFRACTION100
5.6-44.530.19871390.18042934X-RAY DIFFRACTION98.87

+
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