[English] 日本語
Yorodumi
- PDB-4ohm: Human GKRP bound to AMG-0771 and sorbitol-6-phosphate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ohm
TitleHuman GKRP bound to AMG-0771 and sorbitol-6-phosphate
ComponentsGlucokinase regulatory protein
KeywordsCARBOHYDRATE BINDING PROTEIN/INHIBITOR / SIS domain containing protein / Binds and inhibits glucokinase / Glucokinase / liver / CARBOHYDRATE BINDING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of glucokinase activity / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis ...negative regulation of glucokinase activity / fructose-6-phosphate binding / glucose sensor activity / urate metabolic process / kinase inhibitor activity / carbohydrate derivative metabolic process / response to fructose / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / triglyceride homeostasis / enzyme inhibitor activity / response to glucose / protein import into nucleus / glucose homeostasis / carbohydrate binding / carbohydrate metabolic process / enzyme binding / mitochondrion / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2TF / IODIDE ION / D-SORBITOL-6-PHOSPHATE / Glucokinase regulatory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJordan, S.R. / Chmait, S.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Small molecule disruptors of the glucokinase-glucokinase regulatory protein interaction: 3. Structure-activity relationships within the aryl carbinol region of the N-arylsulfonamido-N'-arylpiperazine series.
Authors: Nishimura, N. / Norman, M.H. / Liu, L. / Yang, K.C. / Ashton, K.S. / Bartberger, M.D. / Chmait, S. / Chen, J. / Cupples, R. / Fotsch, C. / Helmering, J. / Jordan, S.R. / Kunz, R.K. / ...Authors: Nishimura, N. / Norman, M.H. / Liu, L. / Yang, K.C. / Ashton, K.S. / Bartberger, M.D. / Chmait, S. / Chen, J. / Cupples, R. / Fotsch, C. / Helmering, J. / Jordan, S.R. / Kunz, R.K. / Pennington, L.D. / Poon, S.F. / Siegmund, A. / Sivits, G. / Lloyd, D.J. / Hale, C. / St Jean, D.J.
History
DepositionJan 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucokinase regulatory protein
B: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,53334
Polymers140,6132
Non-polymers4,91932
Water3,477193
1
A: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,44914
Polymers70,3071
Non-polymers2,14313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,08320
Polymers70,3071
Non-polymers2,77719
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)149.181, 149.181, 132.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

-
Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Glucokinase regulatory protein / / Glucokinase regulator


Mass: 70306.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCKR / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14397
#3: Sugar ChemComp-S6P / D-SORBITOL-6-PHOSPHATE / 1-O-PHOSPHONO-D-GLUCITOL / D-GLUCITOL-6-PHOSPHATE


Type: D-saccharide / Mass: 262.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H15O9P

-
Non-polymers , 5 types, 223 molecules

#2: Chemical ChemComp-2TF / (2S)-2-{4-[(2S)-4-[(6-aminopyridin-3-yl)sulfonyl]-2-(prop-1-yn-1-yl)piperazin-1-yl]phenyl}-3,3,3-trifluoropropane-1,2-diol


Mass: 484.492 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23F3N4O4S
#4: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: I
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Bis-tris, 0.2M NaI, 16%PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Aug 13, 2011 / Details: osmic mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 61260 / % possible obs: 91 % / Observed criterion σ(F): 1

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LY9

4ly9


Resolution: 2.4→37.97 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.224 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27248 3269 5.1 %RANDOM
Rwork0.21508 ---
obs0.21801 61260 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.594 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9075 0 143 193 9411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199357
X-RAY DIFFRACTIONr_bond_other_d0.0010.029163
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9812673
X-RAY DIFFRACTIONr_angle_other_deg0.8843.00121020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95551169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65824.415376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.009151658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3811550
X-RAY DIFFRACTIONr_chiral_restr0.0930.21487
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022038
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_it4.0234.7814694
X-RAY DIFFRACTIONr_mcbond_other4.024.784693
X-RAY DIFFRACTIONr_mcangle_it5.9927.1585857
X-RAY DIFFRACTIONr_mcangle_other5.9917.1585858
X-RAY DIFFRACTIONr_scbond_it4.1715.1514663
X-RAY DIFFRACTIONr_scbond_other4.1055.1464651
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2257.5646799
X-RAY DIFFRACTIONr_long_range_B_refined8.41237.79710696
X-RAY DIFFRACTIONr_long_range_B_other8.41237.79910697
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 219 -
Rwork0.329 4362 -
obs--96.18 %

+
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