[English] 日本語
Yorodumi
- PDB-9kek: human glyoxalase I (with C-ter His tag) in complex with piceatannol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9kek
Titlehuman glyoxalase I (with C-ter His tag) in complex with piceatannol
ComponentsLactoylglutathione lyase
KeywordsLYASE / glyoxalase i / zinc metalloenzyme
Function / homology
Function and homology information


lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / extracellular exosome ...lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal metabolic process / Pyruvate metabolism / glutathione metabolic process / osteoclast differentiation / carbohydrate metabolic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / extracellular exosome / zinc ion binding / nucleoplasm / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Glyoxalase I signature 2. / Glyoxalase I / Glyoxalase I, conserved site / Glyoxalase I signature 1. / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase
Similarity search - Domain/homology
PICEATANNOL / Lactoylglutathione lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsAndo, K. / Yokoyama, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)22K06554 Japan
CitationJournal: To Be Published
Title: Crystal structures of glyoxalase I complexes with nature-derived inhibitors reveal flexible and multiple binding poses
Authors: Ando, K. / Yokoyama, H.
History
DepositionNov 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lactoylglutathione lyase
B: Lactoylglutathione lyase
C: Lactoylglutathione lyase
D: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,27115
Polymers87,4994
Non-polymers1,77111
Water3,837213
1
A: Lactoylglutathione lyase
B: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7578
Polymers43,7502
Non-polymers1,0086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-110 kcal/mol
Surface area15780 Å2
MethodPISA
2
C: Lactoylglutathione lyase
D: Lactoylglutathione lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5137
Polymers43,7502
Non-polymers7645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-122 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.956, 65.758, 69.633
Angle α, β, γ (deg.)90, 96.218, 90
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Lactoylglutathione lyase / Aldoketomutase / Glyoxalase I / Glx I / Ketone-aldehyde mutase / Methylglyoxalase / S-D- ...Aldoketomutase / Glyoxalase I / Glx I / Ketone-aldehyde mutase / Methylglyoxalase / S-D-lactoylglutathione methylglyoxal lyase


Mass: 21874.869 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLO1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04760, lactoylglutathione lyase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PIT / PICEATANNOL / 4-[(E)-2-(3,5-DIHYDROXYPHENYL)ETHENYL]BENZENE-1,2-DIOL


Mass: 244.243 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H12O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Sodium chloride, 0.1 M Bis-Tris, 25%(w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.018 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 26, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.018 Å / Relative weight: 1
ReflectionResolution: 2.11→19.93 Å / Num. obs: 38343 / % possible obs: 100 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.8
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1865 / CC1/2: 0.911 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→19.93 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.684 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.202
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2328 1897 4.951 %
Rwork0.1664 36419 -
all0.17 --
obs-38316 99.758 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.764 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å2-0 Å2-0.865 Å2
2---1.258 Å20 Å2
3----1.214 Å2
Refinement stepCycle: LAST / Resolution: 2.11→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5636 0 110 213 5959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0125871
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165501
X-RAY DIFFRACTIONr_angle_refined_deg2.3451.847901
X-RAY DIFFRACTIONr_angle_other_deg0.7911.78812792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2025704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.282529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.982101050
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.47210263
X-RAY DIFFRACTIONr_chiral_restr0.1180.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026704
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021256
X-RAY DIFFRACTIONr_nbd_refined0.2160.21087
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.25051
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22730
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.23195
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other00.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2740.249
X-RAY DIFFRACTIONr_nbd_other0.3020.2144
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1860.214
X-RAY DIFFRACTIONr_mcbond_it3.7162.3872828
X-RAY DIFFRACTIONr_mcbond_other3.7112.3872828
X-RAY DIFFRACTIONr_mcangle_it5.1384.2623528
X-RAY DIFFRACTIONr_mcangle_other5.1394.2653529
X-RAY DIFFRACTIONr_scbond_it5.1182.8493043
X-RAY DIFFRACTIONr_scbond_other5.1172.853044
X-RAY DIFFRACTIONr_scangle_it7.1285.0024373
X-RAY DIFFRACTIONr_scangle_other7.1275.0034374
X-RAY DIFFRACTIONr_lrange_it8.99528.5916414
X-RAY DIFFRACTIONr_lrange_other928.5046393
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.11-2.1640.2511220.19526370.19727620.9570.97399.89140.169
2.164-2.2230.2681140.18926180.19227340.9580.97599.92680.161
2.223-2.2860.3141450.20225060.20826550.9390.95399.84930.178
2.286-2.3560.2671350.18224300.18725670.9590.97999.92210.156
2.356-2.4320.2371440.17723550.18125000.9560.9899.960.15
2.432-2.5160.2821250.17122940.17624200.9590.98199.95870.147
2.516-2.6090.261210.17922260.18323490.9590.9899.91490.153
2.609-2.7140.2971160.19920930.20422120.9220.96699.86440.171
2.714-2.8320.245940.17720940.1821880.960.981000.154
2.832-2.9670.241850.17319880.17620770.9630.98199.80740.152
2.967-3.1240.2141030.17518600.17719680.9680.98199.74590.156
3.124-3.3090.2561100.17317710.17818900.9620.98399.52380.158
3.309-3.530.224940.1816570.18217540.9720.98399.8290.168
3.53-3.8030.232570.15915860.16116430.9610.9871000.147
3.803-4.1510.2820.13314600.13715420.9740.9891000.125
4.151-4.6160.158780.11112930.11413710.9860.9931000.107
4.616-5.2830.149510.11711940.11812450.9870.9931000.114
5.283-6.3590.214520.1710130.17210650.9770.9861000.161
6.359-8.5680.255440.1768050.188490.9680.9841000.176
8.568-19.930.17250.1775390.1765640.9870.9841000.19

+
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