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- PDB-9keg: human glyoxalase I (with C-ter His tag) in complex with licochalc... -

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Basic information

Entry
Database: PDB / ID: 9keg
Titlehuman glyoxalase I (with C-ter His tag) in complex with licochalcone B, form 2
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
: / BETA-MERCAPTOETHANOL / Lactoylglutathione lyase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,07611
Polymers43,7502
Non-polymers1,3269
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-119 kcal/mol
Surface area15360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.896, 66.131, 41.694
Angle α, β, γ (deg.)90.00, 100.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
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

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Non-polymers , 5 types, 224 molecules

#2: Chemical ChemComp-A1L5R / 1-(4-hydroxyphenyl)-3-[2-methoxy-3,4-bis(oxidanyl)phenyl]prop-2-en-1-one / Licochalcone B


Mass: 286.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2 M Sodium chloride, 0.1 M MES, 25%(w/v) PEG 3350

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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: 1.8→19.74 Å / Num. obs: 34230 / % possible obs: 100 % / Redundancy: 3.5 % / CC1/2: 0.993 / Net I/σ(I): 18.4
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1684 / CC1/2: 0.895

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.74 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 7.547 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23908 1792 5.2 %RANDOM
Rwork0.19367 ---
obs0.19605 32418 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.1 Å2
2---1.24 Å2-0 Å2
3---1.56 Å2
Refinement stepCycle: 1 / Resolution: 1.8→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2800 0 82 215 3097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0122941
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162758
X-RAY DIFFRACTIONr_angle_refined_deg2.3881.8443952
X-RAY DIFFRACTIONr_angle_other_deg0.8111.7866412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5015350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3239.520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52910522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1230.2412
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023352
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02628
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_it2.1941.551406
X-RAY DIFFRACTIONr_mcbond_other2.1931.551406
X-RAY DIFFRACTIONr_mcangle_it3.1852.7661754
X-RAY DIFFRACTIONr_mcangle_other3.1862.7711755
X-RAY DIFFRACTIONr_scbond_it3.3231.881535
X-RAY DIFFRACTIONr_scbond_other3.3221.8811536
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.663.2982199
X-RAY DIFFRACTIONr_long_range_B_refined6.73718.233298
X-RAY DIFFRACTIONr_long_range_B_other6.73718.233299
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 124 -
Rwork0.214 2360 -
obs--100 %
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)
10.64490.0168-0.02390.6856-0.10850.32680.0258-0.0517-0.0940.0104-0.0321-0.0540.0175-0.01570.00630.0043-0.0084-0.00120.0180.00150.024820.344710.84123.3463
20.65350.02410.04590.7269-0.08030.1610.0112-0.023-0.0127-0.0583-0.0010.0086-0.0069-0.0193-0.01020.0131-0.00140.00750.0282-0.00870.011615.300720.5749-2.8209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 183
2X-RAY DIFFRACTION2B8 - 183

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