[English] 日本語
Yorodumi
- PDB-7rcl: Crystal Structure of ADP-bound Galactokinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rcl
TitleCrystal Structure of ADP-bound Galactokinase
ComponentsGalactokinase
KeywordsSUGAR BINDING PROTEIN / GALK / galactokinase / Galactose / ADP / disulfide
Function / homology
Function and homology information


glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / Galactose catabolism / galactose catabolic process via UDP-galactose, Leloir pathway / galactose binding / galactose metabolic process / extracellular exosome ...glycolytic process from galactose / Defective GALK1 causes GALCT2 / galactitol metabolic process / galactokinase / galactokinase activity / Galactose catabolism / galactose catabolic process via UDP-galactose, Leloir pathway / galactose binding / galactose metabolic process / extracellular exosome / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal ...Galactokinase, N-terminal domain / Galactokinase, conserved site / Galactokinase galactose-binding signature / Galactokinase signature. / Galactokinase / Mevalonate/galactokinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / alpha-D-galactopyranose / PHOSPHATE ION / Galactokinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
Model detailsHuman Galactokinase enzyme with ADP bound
AuthorsWhitby, F.G. / Hall, M.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1HD074844 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structure-Based Optimization of Small Molecule Human Galactokinase Inhibitors.
Authors: Liu, L. / Tang, M. / Pragani, R. / Whitby, F.G. / Zhang, Y.Q. / Balakrishnan, B. / Fang, Y. / Karavadhi, S. / Tao, D. / LeClair, C.A. / Hall, M.D. / Marugan, J.J. / Boxer, M. / Shen, M. / ...Authors: Liu, L. / Tang, M. / Pragani, R. / Whitby, F.G. / Zhang, Y.Q. / Balakrishnan, B. / Fang, Y. / Karavadhi, S. / Tao, D. / LeClair, C.A. / Hall, M.D. / Marugan, J.J. / Boxer, M. / Shen, M. / Hill, C.P. / Lai, K. / Patnaik, S.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Galactokinase
B: Galactokinase
C: Galactokinase
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,47531
Polymers168,8124
Non-polymers3,66327
Water7,152397
1
A: Galactokinase
C: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,19015
Polymers84,4062
Non-polymers1,78413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galactokinase
D: Galactokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,28516
Polymers84,4062
Non-polymers1,87914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.901, 114.126, 206.705
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Galactokinase / Galactose kinase


Mass: 42203.020 Da / Num. of mol.: 4 / Mutation: K252A, E253A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALK1, GALK / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: P51570, galactokinase
#2: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 420 molecules

#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 63.67 % / Mosaicity: 0.518 ° / Mosaicity esd: 0.006 °
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: Seeding into drops containing GALK protein at 8 mg/ml, 2.3M Na/K pH6.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1533 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1533 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 86404 / % possible obs: 95.7 % / Redundancy: 11.1 % / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.069 / Rrim(I) all: 0.222 / Χ2: 1.216 / Net I/σ(I): 9 / Num. measured all: 955737
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.4-2.496.185200.3560.7971.26595
2.49-2.596.484860.4310.7231.27895.3
2.59-2.76.884770.5540.6251.24395.1
2.7-2.857.584670.6740.5161.24594.6
2.85-3.02884560.7690.3621.17894.30.953
3.02-3.268.784230.890.2431.24593.60.6810.726
3.26-3.581184130.9630.1481.18993.60.5020.525
3.58-4.11585670.9830.0841.34694.80.3310.342
4.1-5.1720.191360.9910.0511.19699.90.2230.23
5.17-5019.294590.9980.0251.1171000.1070.11

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wuu

1wuu


Resolution: 2.4→39.63 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 16.248 / SU ML: 0.178 / SU R Cruickshank DPI: 0.2564 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 1726 2 %RANDOM
Rwork0.1732 ---
obs0.1743 84573 95.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 153.74 Å2 / Biso mean: 56.893 Å2 / Biso min: 30.76 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20 Å2
2--2.51 Å20 Å2
3----0.47 Å2
Refinement stepCycle: final / Resolution: 2.4→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11800 0 219 397 12416
Biso mean--68.48 54.92 -
Num. residues----1564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01312354
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711462
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.64816806
X-RAY DIFFRACTIONr_angle_other_deg1.4161.56926503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.77651582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16620.368653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63151971
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.61715125
X-RAY DIFFRACTIONr_chiral_restr0.0870.21591
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214030
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022622
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 124 -
Rwork0.278 6093 -
all-6217 -
obs--94.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8948-0.0228-0.28560.11960.22070.59170.02050.2652-0.01690.0581-0.011-0.0291-0.0171-0.1137-0.00950.14540.0354-0.04660.3195-0.00230.032921.0799-26.7385-5.9596
20.33140.1422-0.05030.1865-0.31870.8678-0.05110.01450.05840.05050.01930.0042-0.0185-0.07640.03180.20630.039-0.01610.2150.02650.053115.8466-32.131748.1
30.008-0.0041-0.04040.4410.80031.82380.01660.02330.00280.11550.0876-0.01150.30440.1697-0.10420.22020.0764-0.03040.2805-0.06220.031922.9339-61.6998-0.9639
40.44520.3684-0.24480.4901-0.43081.11850.08890.03540.02490.3127-0.15390.0117-0.32920.12550.0650.4206-0.1697-0.04040.202-0.01370.021836.8722-4.460844.5445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 401
2X-RAY DIFFRACTION2B2 - 401
3X-RAY DIFFRACTION3C2 - 401
4X-RAY DIFFRACTION4D2 - 401

+
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