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- PDB-9hjn: Structure of UDP-Galactose-4-epimerase (GalE) bound to fragment f... -

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Basic information

Entry
Database: PDB / ID: 9hjn
TitleStructure of UDP-Galactose-4-epimerase (GalE) bound to fragment from Diamond XChem experiment.
ComponentsUDP-glucose 4-epimerase
KeywordsCARBOHYDRATE / Fragment / Epimerase / Carbohydrate processing
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
N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea / MALONATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsBrowne, W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute 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. / Purkiss, A.G. / Weckwerth, T. / Ogrodowicz, R. / Prema, R. / Kunzelmann, S. / Roustan, C. / Mouilleron, S. / Schumann, B.
History
DepositionNov 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 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
B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,20516
Polymers76,6492
Non-polymers2,55514
Water6,882382
1
A: UDP-glucose 4-epimerase
hetero molecules

B: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,20516
Polymers76,6492
Non-polymers2,55514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area6330 Å2
ΔGint-13 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.144, 108.327, 137.447
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

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

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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

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Components

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Protein , 1 types, 2 molecules AB

#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: 38324.605 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 , 7 types, 396 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-JGA / N-ethyl-N'-(5-methyl-1,2-oxazol-3-yl)urea


Mass: 169.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 2.24 Å3/Da / Density % sol: 45.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 18% PEG 3350 0.2 M Sodium Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.7838 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 6, 2023 / Details: mirrors
RadiationMonochromator: Double CrystaL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7838 Å / Relative weight: 1
ReflectionResolution: 1.65→43.72 Å / Num. obs: 160447 / % possible obs: 99.4 % / Redundancy: 7.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.44 / Rpim(I) all: 0.173 / Rrim(I) all: 0.473 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
4.86-43.737.40.09727.164140.9960.0380.104100
1.65-1.688.2890.779300.0713.2238.999.27

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.88)refinement
DIALS3.8data reduction
DIALS3.8data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.651→43.72 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.784 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.103 / ESU R Free: 0.1 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2188 4221 5.066 %
Rwork0.1896 79097 -
all0.191 --
obs-83318 99.597 %
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: 23.482 Å2
Baniso -1Baniso -2Baniso -3
1--1.258 Å20 Å2-0 Å2
2--1.119 Å20 Å2
3---0.139 Å2
Refinement stepCycle: LAST / Resolution: 1.651→43.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5270 0 167 382 5819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125561
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.8217528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7615686
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.649542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.910881
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.30210245
X-RAY DIFFRACTIONr_chiral_restr0.1080.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024252
X-RAY DIFFRACTIONr_nbd_refined0.2030.22609
X-RAY DIFFRACTIONr_nbtor_refined0.3130.23785
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2370
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2640.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.218
X-RAY DIFFRACTIONr_mcbond_it1.8392.1152746
X-RAY DIFFRACTIONr_mcangle_it2.5713.7933430
X-RAY DIFFRACTIONr_scbond_it3.1812.3962815
X-RAY DIFFRACTIONr_scangle_it4.6984.2264098
X-RAY DIFFRACTIONr_lrange_it6.23427.82724752
X-RAY DIFFRACTIONr_ncsr_local_group_10.090.0510932
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.090310.05009
12BX-RAY DIFFRACTIONLocal ncs0.090310.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.651-1.6940.3252850.3115736X-RAY DIFFRACTION98.932
1.694-1.740.3093010.2925599X-RAY DIFFRACTION99.4438
1.74-1.7910.2562890.2595490X-RAY DIFFRACTION99.6208
1.791-1.8460.2612840.255357X-RAY DIFFRACTION99.6819
1.846-1.9060.2472750.2245138X-RAY DIFFRACTION99.742
1.906-1.9730.2462540.2095003X-RAY DIFFRACTION99.6777
1.973-2.0470.2442750.1964814X-RAY DIFFRACTION99.843
2.047-2.130.2142600.1844678X-RAY DIFFRACTION99.8181
2.13-2.2250.2112510.1724463X-RAY DIFFRACTION99.8729
2.225-2.3330.2072200.1754309X-RAY DIFFRACTION99.9338
2.333-2.4590.2211920.1784120X-RAY DIFFRACTION99.9536
2.459-2.6080.2271970.1793882X-RAY DIFFRACTION99.9755
2.608-2.7870.2032080.1813665X-RAY DIFFRACTION100
2.787-3.0090.1971610.1713301X-RAY DIFFRACTION96.3272
3.009-3.2950.1821880.173178X-RAY DIFFRACTION100
3.295-3.6810.2011720.1762828X-RAY DIFFRACTION100
3.681-4.2460.1911480.1612550X-RAY DIFFRACTION100
4.246-5.1880.1851140.1562203X-RAY DIFFRACTION100
5.188-7.2860.2651020.2051719X-RAY DIFFRACTION100
7.286-43.720.223450.1921063X-RAY DIFFRACTION99.8198

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