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- PDB-29ls: PanDDA analysis - Crystal structure of the Ubiquitin conjugating ... -

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Basic information

Entry
Database: PDB / ID: 29ls
TitlePanDDA analysis - Crystal structure of the Ubiquitin conjugating enzyme 4 from Leishmania major (LmUbC4) in complex with Z240654968
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 / N-(2-chloropyridin-3-yl)butanamide / Ubiquitin-conjugating enzyme E2 H
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.219 Å
AuthorsExertier, C. / Fiorillo, A. / Ilari, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
iNEXT-DiscoveryPID 32193European Union
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
DepositionMar 20, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)38,8018
Polymers38,3912
Non-polymers4106
Water66737
1
A: Ubiquitin-conjugating enzyme E2 H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4654
Polymers19,1961
Non-polymers2703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin-conjugating enzyme E2 H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3364
Polymers19,1961
Non-polymers1403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.813, 115.813, 154.377
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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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 defined enough to unambiguously reconstruct the N- 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-WNS / N-(2-chloropyridin-3-yl)butanamide


Mass: 198.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11ClN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 3.1 M NaCl, 0.1 M MES/imid pH 6.5, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.921344 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921344 Å / Relative weight: 1
ReflectionResolution: 2.219→61.19 Å / Num. obs: 19922 / % possible obs: 100 % / Redundancy: 20.6 % / Biso Wilson estimate: 76.29 Å2 / CC1/2: 1 / Net I/σ(I): 20
Reflection shellResolution: 2.22→2.26 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 945 / CC1/2: 0.39 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
DIMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.219→22.76 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.306 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.297 / SU Rfree Blow DPI: 0.223 / SU Rfree Cruickshank DPI: 0.228
RfactorNum. reflection% reflectionSelection details
Rfree0.2759 993 4.99 %RANDOM
Rwork0.2461 ---
obs0.2476 1776 99.9 %-
Displacement parametersBiso mean: 100.42 Å2
Baniso -1Baniso -2Baniso -3
1-8.2974 Å20 Å20 Å2
2--8.2974 Å20 Å2
3----16.5947 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.219→22.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2565 0 22 38 2625
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072830HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.853884HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d970SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes500HARMONIC5
X-RAY DIFFRACTIONt_it2817HARMONIC10
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.94
X-RAY DIFFRACTIONt_other_torsion18.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion350SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2005SEMIHARMONIC4
LS refinement shellResolution: 2.22→2.24 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.4927 -3.69 %
Rwork0.4716 391 -
all0.4723 406 -
obs--96.61 %
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)
13.4072-1.0059-0.37073.55780.4010.5187-0.1263-0.0386-0.3859-0.10920.00180.12070.0451-0.1120.1245-0.0483-0.0230.0552-0.1099-0.03460.1372-4.7434-17.5366-51.6538
25.93351.4591-1.51342.6248-0.50791.42270.0876-1.038-0.65780.658-0.2484-0.03980.18620.1430.16090.2949-0.00230.08990.22040.4029-0.2808-2.9285-18.5857-19.4492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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