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- PDB-9hi1: STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COMP... -

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Basic information

Entry
Database: PDB / ID: 9hi1
TitleSTRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COMPOUND WBX09
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
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 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)78,51718
Polymers75,7862
Non-polymers2,73016
Water10,467581
1
A: UDP-glucose 4-epimerase
hetero molecules

B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,51718
Polymers75,7862
Non-polymers2,73016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area6870 Å2
ΔGint5 kcal/mol
Surface area26340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.147, 110.205, 135.411
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 3 - 344 / Label seq-ID: 2 - 343

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#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: 37893.102 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
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / 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-A1IU5 / 3-[(5-cyclobutyl-1,2-oxazol-3-yl)carbamoylamino]-~{N}-pyridin-4-yl-propanamide


Mass: 329.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H19N5O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.49 %
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 / Wavelength: 0.7098 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Jul 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7098 Å / Relative weight: 1
ReflectionResolution: 0.95→57.76 Å / Num. obs: 415408 / % possible obs: 99.4 % / Redundancy: 40 % / CC1/2: 1 / Net I/σ(I): 76.5
Reflection shellResolution: 0.95→0.97 Å / Num. unique obs: 22430 / CC1/2: 0.33

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
DIALSdata reduction
xia2.multiplexdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→57.755 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.5 / SU ML: 0.025 / Cross valid method: FREE R-VALUE / ESU R: 0.023 / ESU R Free: 0.023 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.189 2000 0.49 %
Rwork0.1811 406081 -
all0.181 --
obs-408081 94.531 %
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: 15.018 Å2
Baniso -1Baniso -2Baniso -3
1--0.327 Å2-0 Å20 Å2
2--0.286 Å20 Å2
3---0.041 Å2
Refinement stepCycle: LAST / Resolution: 0.95→57.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5282 0 184 581 6047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125921
X-RAY DIFFRACTIONr_angle_refined_deg2.1051.8268063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.4796.250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3110973
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.22210259
X-RAY DIFFRACTIONr_chiral_restr0.1240.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024553
X-RAY DIFFRACTIONr_nbd_refined0.2090.22827
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23939
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2428
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2170.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1560.228
X-RAY DIFFRACTIONr_mcbond_it1.3291.2522885
X-RAY DIFFRACTIONr_mcangle_it1.9212.2613629
X-RAY DIFFRACTIONr_scbond_it2.5071.4673036
X-RAY DIFFRACTIONr_scangle_it3.3992.5824396
X-RAY DIFFRACTIONr_lrange_it4.45916.6219313
X-RAY DIFFRACTIONr_ncsr_local_group_10.1240.0511095
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.124490.05007
12AX-RAY DIFFRACTIONLocal ncs0.124490.05007
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
0.95-0.9750.3461160.379233940.379317050.8940.88174.15230.377
0.975-1.0020.3441360.364277830.364309190.9160.89490.29720.36
1.002-1.0310.371390.332282150.332300250.9180.91594.43460.326
1.031-1.0620.3091360.288274930.288291420.9230.93194.80820.282
1.062-1.0970.2551320.249268830.249283910.9530.95695.15340.239
1.097-1.1360.2011270.22259940.22273740.9750.96795.42270.204
1.136-1.1780.2271260.204252340.204264780.9630.97395.77760.183
1.178-1.2270.2151190.193243450.194254520.9720.97696.11820.171
1.227-1.2810.1951160.185235500.185245360.9760.97896.45420.16
1.281-1.3440.1661110.175224930.175233600.980.9896.76370.151
1.344-1.4160.1991060.171214810.172222420.9770.98197.05510.147
1.416-1.5020.1771000.165204960.165211480.9810.98397.38980.14
1.502-1.6060.177960.15193110.15198620.980.98697.70920.129
1.606-1.7340.154890.154180610.154185250.9860.98597.97570.134
1.734-1.90.173820.162167400.163171130.9830.98498.29950.145
1.9-2.1240.188750.174152160.174155080.9780.98298.60070.163
2.124-2.4520.153660.169135340.169137500.9870.98398.90910.163
2.452-3.0010.197580.175115350.175116910.9760.98199.16180.177
3.001-4.2390.181450.15790920.15791900.9820.98599.42330.173
4.239-57.7550.164250.18452320.18452780.9850.97999.60210.224

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