[English] 日本語
Yorodumi
- PDB-5hfu: Crystal Structure of Human Hexokinase 2 with cmpd 27, a 2-amido-6... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hfu
TitleCrystal Structure of Human Hexokinase 2 with cmpd 27, a 2-amido-6-benzenesulfonamide glucosamine
ComponentsHexokinase-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / metabolism / inhibitor complex / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of mitochondrial membrane permeability / hexokinase activity / maintenance of protein location in mitochondrion / regulation of glucose import / establishment of protein localization to mitochondrion / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity ...negative regulation of mitochondrial membrane permeability / hexokinase activity / maintenance of protein location in mitochondrion / regulation of glucose import / establishment of protein localization to mitochondrion / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / D-glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / intracellular glucose homeostasis / apoptotic mitochondrial changes / negative regulation of reactive oxygen species metabolic process / lactation / cellular response to leukemia inhibitory factor / sarcoplasmic reticulum / response to ischemia / glycolytic process / positive regulation of angiogenesis / glucose metabolic process / mitochondrial outer membrane / response to hypoxia / intracellular membrane-bounded organelle / centrosome / mitochondrion / ATP binding / membrane / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-603 / Hexokinase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.923 Å
AuthorsCampobasso, N. / Zhao, B. / Smallwood, A.
CitationJournal: Acs Med.Chem.Lett. / Year: 2016
Title: Discovery of a Novel 2,6-Disubstituted Glucosamine Series of Potent and Selective Hexokinase 2 Inhibitors.
Authors: Lin, H. / Zeng, J. / Xie, R. / Schulz, M.J. / Tedesco, R. / Qu, J. / Erhard, K.F. / Mack, J.F. / Raha, K. / Rendina, A.R. / Szewczuk, L.M. / Kratz, P.M. / Jurewicz, A.J. / Cecconie, T. / ...Authors: Lin, H. / Zeng, J. / Xie, R. / Schulz, M.J. / Tedesco, R. / Qu, J. / Erhard, K.F. / Mack, J.F. / Raha, K. / Rendina, A.R. / Szewczuk, L.M. / Kratz, P.M. / Jurewicz, A.J. / Cecconie, T. / Martens, S. / McDevitt, P.J. / Martin, J.D. / Chen, S.B. / Jiang, Y. / Nickels, L. / Schwartz, B.J. / Smallwood, A. / Zhao, B. / Campobasso, N. / Qian, Y. / Briand, J. / Rominger, C.M. / Oleykowski, C. / Hardwicke, M.A. / Luengo, J.I.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hexokinase-2
B: Hexokinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,2996
Polymers206,2052
Non-polymers2,0944
Water1,02757
1
A: Hexokinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1503
Polymers103,1031
Non-polymers1,0472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hexokinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1503
Polymers103,1031
Non-polymers1,0472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.883, 154.986, 114.205
Angle α, β, γ (deg.)90.00, 95.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Hexokinase-2 / Hexokinase type II / HK II / Muscle form hexokinase


Mass: 103102.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52789, hexokinase
#2: Chemical
ChemComp-603 / ~{N}-[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-[[(4-cyanophenyl)sulfonylamino]methyl]-2,4,5-tris(oxidanyl)oxan-3-yl]-3-phenyl-benzamide


Mass: 523.558 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H25N3O7S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6
Details: protein: 10mgs/mL in 50mM TrisHCL pH = 7.5, 250mM NaCl, 2mM DTT, 2mM MgCl2 Well solution: 0.1M Na Citrate pH = 6, 16 % PEG3350, 10 % Ethylene glycol Cryo: 20 % ethylene glycol in well
PH range: 5 - 6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.92→113.64 Å / Num. obs: 49230 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 11.2

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.923→113.64 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.252 2398 4.88 %
Rwork0.1824 --
obs0.1857 49178 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.923→113.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13754 0 148 57 13959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914138
X-RAY DIFFRACTIONf_angle_d1.24519063
X-RAY DIFFRACTIONf_dihedral_angle_d14.5458451
X-RAY DIFFRACTIONf_chiral_restr0.0612133
X-RAY DIFFRACTIONf_plane_restr0.0072505

+
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://pdbjlvh1.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