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- PDB-28ht: Crystal structure of the Ubiquitin Conjugating Enzyme 4 from Leis... -

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Basic information

Entry
Database: PDB / ID: 28ht
TitleCrystal structure of the Ubiquitin Conjugating Enzyme 4 from Leishmania major (LmUbC4)
ComponentsUbiquitin-conjugating enzyme E2 H
KeywordsLIGASE / Ubiquitin conjugating enzyme
Function / homology
Function and homology information


ubiquitin conjugating enzyme activity / protein polyubiquitination / ATP binding
Similarity search - Function
Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
IMIDAZOLE / Ubiquitin-conjugating enzyme E2 H
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsExertier, C. / Fiorillo, A. / Ilari, A. / Antonelli, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
Ministero dell Universita e della RicercaIR0000009 Italy
CitationJournal: Acs Omega / Year: 2026
Title: UbC4 from Leishmania is a Druggable E2 Ubiquitin Conjugating Enzyme: Structural Basis and Fragment Hits for Future E2-Recruiting PROTAC Development.
Authors: Exertier, C. / Antonelli, L. / Liuzzi, A. / Ruffa, M. / Brufani, V. / Colotti, G. / Fiorillo, A. / Ilari, A.
History
DepositionJan 30, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme E2 H
B: Ubiquitin-conjugating enzyme E2 H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8779
Polymers38,3912
Non-polymers4857
Water88349
1
A: Ubiquitin-conjugating enzyme E2 H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6127
Polymers19,1961
Non-polymers4166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2652
Polymers19,1961
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.000, 115.000, 151.542
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-414-

HOH

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 H / (E3-independent) E2 ubiquitin-conjugating enzyme H / E2 ubiquitin-conjugating enzyme H / Ubiquitin ...(E3-independent) E2 ubiquitin-conjugating enzyme H / E2 ubiquitin-conjugating enzyme H / Ubiquitin carrier protein H / Ubiquitin-protein ligase H


Mass: 19195.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The electronic density is not well enough defined to unambiguously reconstruct the N-terminal and C-terminal extremities
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_32_0700 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4Q5L3
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 3 M NaCl, 0.1 M MES/imidazole pH 6.5, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.157→83.23 Å / Num. obs: 20142 / % possible obs: 95.9 % / Redundancy: 18.9 % / CC1/2: 0.998 / Net I/σ(I): 20.1
Reflection shellResolution: 2.157→2.194 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1051 / CC1/2: 0.357 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0431refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→83.23 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / SU B: 16.1 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22424 939 4.7 %RANDOM
Rwork0.19114 ---
obs0.19243 19106 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.612 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å2-0 Å2
2--0.31 Å20 Å2
3----1 Å2
Refinement stepCycle: 1 / Resolution: 2.16→83.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2583 0 30 49 2662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122731
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162474
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.833725
X-RAY DIFFRACTIONr_angle_other_deg0.4861.765713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.288524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23510425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02663
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_it3.0595.1441283
X-RAY DIFFRACTIONr_mcbond_other3.0265.1461283
X-RAY DIFFRACTIONr_mcangle_it4.6529.2281603
X-RAY DIFFRACTIONr_mcangle_other4.6589.2321604
X-RAY DIFFRACTIONr_scbond_it3.8555.6251448
X-RAY DIFFRACTIONr_scbond_other3.8545.6291449
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.28510.0882119
X-RAY DIFFRACTIONr_long_range_B_refined8.34747.742929
X-RAY DIFFRACTIONr_long_range_B_other8.34647.582925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 90 -
Rwork0.371 1430 -
obs--99.87 %
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)
10.9612-0.4117-0.02871.17990.27470.1363-0.0856-0.0708-0.2363-0.09920.02750.0887-0.038-0.04360.05810.06490.00660.02820.0358-0.02230.5381-5.076-17.698-51.295
22.12990.4492-0.71490.4793-0.01590.5980.1744-0.3521-0.4010.0847-0.2081-0.0547-0.13240.05380.03380.1753-0.02940.0170.19260.20190.3408-2.614-18.504-18.7
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 205
2X-RAY DIFFRACTION2B13 - 201

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