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- PDB-8jvl: Identification and characterization of inhibitors covalently modi... -

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Basic information

Entry
Database: PDB / ID: 8jvl
TitleIdentification and characterization of inhibitors covalently modifying catalytic cysteine of UBE2T and blocking ubiquitin transfer
ComponentsUbiquitin-conjugating enzyme E2 T
KeywordsLIGASE/INHIBITOR / UBE2T / structure / drug discovery / covalent inhibitor / Fanconi anemia / LIGASE-inhibitor complex
Function / homology
Function and homology information


protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein monoubiquitination / protein K48-linked ubiquitination / protein autoubiquitination ...protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein monoubiquitination / protein K48-linked ubiquitination / protein autoubiquitination / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Fanconi Anemia Pathway / protein polyubiquitination / ubiquitin-protein transferase activity / DNA repair / DNA damage response / ubiquitin protein ligase binding / chromatin binding / nucleolus / nucleoplasm / ATP binding / nucleus
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
1-(4-methoxyphenyl)-1,2,3,4-tetrazole / Ubiquitin-conjugating enzyme E2 T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsAnantharajan, J. / Baburajendran, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2023
Title: Identification and characterization of inhibitors covalently modifying catalytic cysteine of UBE2T and blocking ubiquitin transfer.
Authors: Anantharajan, J. / Tan, Q.W. / Fulwood, J. / Sifang, W. / Huang, Q. / Ng, H.Q. / Koh, X. / Xu, W. / Cherian, J. / Baburajendran, N. / Kang, C. / Ke, Z.
History
DepositionJun 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 29, 2023Provider: 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 T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0693
Polymers17,8311
Non-polymers2382
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint4 kcal/mol
Surface area8480 Å2
Unit cell
Length a, b, c (Å)54.890, 54.890, 184.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

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Components

#1: Protein Ubiquitin-conjugating enzyme E2 T / E2 ubiquitin-conjugating enzyme T / Ubiquitin carrier protein T / Ubiquitin-protein ligase T


Mass: 17830.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2T / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NPD8, E2 ubiquitin-conjugating enzyme
#2: Chemical ChemComp-V5L / 1-(4-methoxyphenyl)-1,2,3,4-tetrazole


Mass: 176.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.89 Å3/Da / Density % sol: 68.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.8 M Sodium formate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 2.06→47.14 Å / Num. obs: 18267 / % possible obs: 99.6 % / Redundancy: 25.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.017 / Rpim(I) all: 0.028 / Rrim(I) all: 0.144 / Χ2: 0.54 / Net I/σ(I): 15.6 / Num. measured all: 467470
Reflection shellResolution: 2.06→2.12 Å / % possible obs: 94.8 % / Redundancy: 24.4 % / Rmerge(I) obs: 2.05 / Num. measured all: 32302 / Num. unique obs: 1322 / CC1/2: 0.871 / Rpim(I) all: 0.409 / Rrim(I) all: 0.02092 / Χ2: 0.46 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→47.14 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2265 1813 10 %
Rwork0.2037 --
obs0.2061 18128 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 17 104 1343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.855
X-RAY DIFFRACTIONf_dihedral_angle_d15.379171
X-RAY DIFFRACTIONf_chiral_restr0.051186
X-RAY DIFFRACTIONf_plane_restr0.008229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.120.30051320.27241183X-RAY DIFFRACTION96
2.12-2.180.27591350.24411208X-RAY DIFFRACTION100
2.18-2.250.27541350.2551220X-RAY DIFFRACTION100
2.25-2.330.30721370.24781231X-RAY DIFFRACTION100
2.33-2.430.25491380.23431244X-RAY DIFFRACTION100
2.43-2.540.25751350.22561226X-RAY DIFFRACTION100
2.54-2.670.26491390.22331248X-RAY DIFFRACTION100
2.67-2.840.2681380.23871243X-RAY DIFFRACTION100
2.84-3.060.25751400.23931262X-RAY DIFFRACTION100
3.06-3.360.25811400.21151251X-RAY DIFFRACTION100
3.36-3.850.19491420.19471287X-RAY DIFFRACTION100
3.85-4.850.19111460.15721310X-RAY DIFFRACTION100
4.86-47.140.18561560.18471402X-RAY DIFFRACTION100

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