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- PDB-9hi0: STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COMP... -

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Basic information

Entry
Database: PDB / ID: 9hi0
TitleSTRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COMPOUND WBX04
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / glycosylation / metabolism / nucleotide-sugar
Function / homology
Function and homology information


Defective GALE causes EDG / UDP-N-acetylglucosamine 4-epimerase activity / UDP-N-acetylglucosamine 4-epimerase / galactose catabolic process / Galactose catabolism / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
UDP-glucose 4-epimerase / GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / D-MALATE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsMouilleron, S. / Schumann, B. / Browne, W. / Purkiss, A. / Weckwerth, T. / Ogrodowicz, R. / Prema, R. / Kunzelmann, S. / Roustan, C.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/S023518/1 United Kingdom
The Francis Crick InstituteCC2127 United Kingdom
The Francis Crick InstituteCC2127 United Kingdom
Wellcome TrustCC2127 United Kingdom
CitationJournal: To Be Published
Title: Identification of Novel Inhibitors of Human UDP-Galactose-4-Epimerase (GalE) by Fragment-Based Lead Discovery
Authors: Browne, W. / Schumann, B. / Purkiss, A. / Weckwerth, T. / Ogrodowicz, R. / Prema, R. / Kunzelmann, S. / Roustan, C. / Mouilleron, S.
History
DepositionNov 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: UDP-glucose 4-epimerase
A: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,31012
Polymers75,9602
Non-polymers2,35010
Water9,440524
1
B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0575
Polymers37,9801
Non-polymers1,0774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2537
Polymers37,9801
Non-polymers1,2736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)136.358, 46.3, 110.727
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein UDP-glucose 4-epimerase / Galactowaldenase / UDP-N-acetylgalactosamine 4-epimerase / UDP-GalNAc 4-epimerase / UDP-N- ...Galactowaldenase / UDP-N-acetylgalactosamine 4-epimerase / UDP-GalNAc 4-epimerase / UDP-N-acetylglucosamine 4-epimerase / UDP-GlcNAc 4-epimerase / UDP-galactose 4-epimerase


Mass: 37980.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GALE / Production host: Escherichia coli (E. coli)
References: UniProt: Q14376, UDP-glucose 4-epimerase, UDP-N-acetylglucosamine 4-epimerase

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Non-polymers , 5 types, 534 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-A1IU2 / 3-[(5-methyl-1,2-oxazol-3-yl)carbamoylamino]-~{N}-pyridin-4-yl-propanamide


Mass: 289.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H15N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 524 / 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: 2.3 Å3/Da / Density % sol: 46.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18% PEG 3350 0.2 M Na Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9212 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 1.37→68.272 Å / Num. obs: 143992 / % possible obs: 97.4 % / Redundancy: 73.3 % / CC1/2: 0.96 / Net I/σ(I): 12.5
Reflection shellResolution: 1.37→1.39 Å / Num. unique obs: 6623 / CC1/2: 0.41

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→68.272 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.996 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.059 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1897 7068 4.922 %
Rwork0.1538 136543 -
all0.156 --
obs-143611 97.095 %
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: 21.462 Å2
Baniso -1Baniso -2Baniso -3
1-0.203 Å2-0 Å20 Å2
2--0.745 Å2-0 Å2
3----0.948 Å2
Refinement stepCycle: LAST / Resolution: 1.37→68.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5311 0 159 524 5994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0125655
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165294
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.8287664
X-RAY DIFFRACTIONr_angle_other_deg0.6131.75312174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1155705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.5576.17651
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg4.468.33318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62410923
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.54310249
X-RAY DIFFRACTIONr_chiral_restr0.0950.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021337
X-RAY DIFFRACTIONr_nbd_refined0.2110.21010
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.24449
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22718
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22844
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1140.213
X-RAY DIFFRACTIONr_nbd_other0.150.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.228
X-RAY DIFFRACTIONr_mcbond_it4.8221.952778
X-RAY DIFFRACTIONr_mcbond_other4.8131.952778
X-RAY DIFFRACTIONr_mcangle_it6.8033.5143476
X-RAY DIFFRACTIONr_mcangle_other6.8033.5163477
X-RAY DIFFRACTIONr_scbond_it6.2632.1872877
X-RAY DIFFRACTIONr_scbond_other6.2592.1872877
X-RAY DIFFRACTIONr_scangle_it8.7953.9034181
X-RAY DIFFRACTIONr_scangle_other8.7943.9034182
X-RAY DIFFRACTIONr_lrange_it11.36421.5816249
X-RAY DIFFRACTIONr_lrange_other11.36421.5826250
X-RAY DIFFRACTIONr_rigid_bond_restr3.667310949
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
1.37-1.4060.3664800.36190890.361108260.8950.89888.38910.358
1.406-1.4440.3354730.34594080.345105460.9070.90793.69430.343
1.444-1.4860.3255150.30793840.308102560.9240.93196.51910.306
1.486-1.5320.2554550.24991680.24999340.9550.95596.86930.245
1.532-1.5820.2364810.19989540.20197070.9630.97397.19790.189
1.582-1.6370.2144510.16686520.16993420.9710.9897.44170.153
1.637-1.6990.24190.14484280.14790620.9720.98597.62750.128
1.699-1.7680.1964250.12980840.13286970.9750.98997.83830.109
1.768-1.8470.1613940.11378330.11584040.9830.99297.89390.093
1.847-1.9370.1833930.11774520.12179830.9780.99198.27130.097
1.937-2.0420.1793660.11471590.11776190.980.99298.76620.095
2.042-2.1660.1563520.11368130.11572410.9840.99298.95040.096
2.166-2.3150.1633570.12163740.12368410.9810.99198.3920.104
2.315-2.50.1682840.11859980.12163200.9820.99199.39870.103
2.5-2.7380.1633100.12855410.1359020.9830.9999.13590.114
2.738-3.0610.172410.13750660.13953240.9820.98899.68070.125
3.061-3.5330.1882330.15144900.15347430.9780.98599.57830.147
3.533-4.3240.1511920.14538370.14540420.9870.98899.67840.15
4.324-6.1040.2031510.1630310.16231850.9780.98799.90580.176
6.104-68.2720.24960.23917820.23918780.9640.961000.262

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