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- PDB-9hi2: STRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COVA... -

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Basic information

Entry
Database: PDB / ID: 9hi2
TitleSTRUCTURE OF HUMAN UDP-GALACTOSE 4-EPIMERASE IN COMPLEX WITH COVALENT COMPOUND WBC10
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 / UDP-glucose 4-epimerase / UDP-glucose 4-epimerase activity / galactose catabolic process via UDP-galactose, Leloir pathway / Galactose catabolism / 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
: / 1,4-DIHYDRONICOTINAMIDE 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,3423
Polymers38,3241
Non-polymers1,0192
Water5,783321
1
A: UDP-glucose 4-epimerase
hetero molecules

A: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6856
Polymers76,6472
Non-polymers2,0384
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5870 Å2
ΔGint-25 kcal/mol
Surface area26150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.040, 114.140, 130.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+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: 38323.582 Da / Num. of mol.: 1
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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Chemical ChemComp-A1IU6 / 3-[[(5-cyclobutyl-1,2-oxazol-3-yl)carbamoylamino]methyl]benzenesulfonyl fluoride


Mass: 353.369 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16FN3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 22.7% PEG 3350 0.2 M NaSO4 0.1 Bis-Tris propane pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.82 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82 Å / Relative weight: 1
ReflectionResolution: 1.37→57.07 Å / Num. obs: 77616 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 18.32 Å2 / CC1/2: 0.3 / Net I/σ(I): 7.9
Reflection shellResolution: 1.37→1.39 Å / Num. unique obs: 4002 / CC1/2: 0.3

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→57.07 Å / SU ML: 0.1514 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.8702
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1743 3945 5.08 %
Rwork0.1406 73663 -
obs0.1423 77608 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.54 Å2
Refinement stepCycle: LAST / Resolution: 1.37→57.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 67 321 3037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01592807
X-RAY DIFFRACTIONf_angle_d1.47983820
X-RAY DIFFRACTIONf_chiral_restr0.0987415
X-RAY DIFFRACTIONf_plane_restr0.0128493
X-RAY DIFFRACTIONf_dihedral_angle_d15.61961071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.32261510.28632688X-RAY DIFFRACTION99.79
1.39-1.40.30431450.2752570X-RAY DIFFRACTION99.78
1.4-1.420.3131400.2592646X-RAY DIFFRACTION99.75
1.42-1.440.28651540.2462619X-RAY DIFFRACTION99.78
1.44-1.460.29861440.23752632X-RAY DIFFRACTION99.89
1.46-1.480.28221340.22312649X-RAY DIFFRACTION99.82
1.48-1.510.22991380.19942620X-RAY DIFFRACTION99.78
1.51-1.530.24731190.18512640X-RAY DIFFRACTION99.75
1.53-1.560.22881670.18042659X-RAY DIFFRACTION99.79
1.56-1.590.20511480.16362600X-RAY DIFFRACTION99.89
1.59-1.620.20421270.15452646X-RAY DIFFRACTION99.64
1.62-1.650.23691320.1422663X-RAY DIFFRACTION99.54
1.65-1.690.21171260.14272637X-RAY DIFFRACTION99.28
1.69-1.730.18321460.1322638X-RAY DIFFRACTION99.11
1.73-1.770.17551550.12592595X-RAY DIFFRACTION98.81
1.77-1.820.16761410.12692582X-RAY DIFFRACTION98.2
1.82-1.870.19451460.12522633X-RAY DIFFRACTION98.93
1.87-1.930.18931360.12222675X-RAY DIFFRACTION99.54
1.93-20.17771550.11872627X-RAY DIFFRACTION99.46
2-2.080.15731270.11142667X-RAY DIFFRACTION99.29
2.08-2.170.14111620.10912615X-RAY DIFFRACTION99.07
2.17-2.290.15121460.10732652X-RAY DIFFRACTION98.83
2.29-2.430.1611340.11022629X-RAY DIFFRACTION98.86
2.43-2.620.13171350.11452664X-RAY DIFFRACTION97.97
2.62-2.880.15821370.12782606X-RAY DIFFRACTION96.96
2.88-3.30.15021350.13692571X-RAY DIFFRACTION94.62
3.3-4.160.14841350.132592X-RAY DIFFRACTION94.13
4.16-57.070.16891300.15722648X-RAY DIFFRACTION92.48

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