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- PDB-8juc: Identification of small-molecule binding sites of a ubiquitin-con... -

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Basic information

Entry
Database: PDB / ID: 8juc
TitleIdentification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening
ComponentsUbiquitin-conjugating enzyme E2 T
KeywordsLIGASE / UBE2T / ubiquitination / fragment-based drug discovery
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 / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination ...protein K29-linked ubiquitination / protein K27-linked ubiquitination / protein K6-linked ubiquitination / protein K11-linked ubiquitination / E2 ubiquitin-conjugating enzyme / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / 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, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like
Similarity search - Domain/homology
: / Ubiquitin-conjugating enzyme E2 T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsAnantharajan, J. / Baburajendran, N.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2024
Title: Identification of small-molecule binding sites of a ubiquitin-conjugating enzyme-UBE2T through fragment-based screening.
Authors: Loh, Y.Y. / Anantharajan, J. / Huang, Q. / Xu, W. / Fulwood, J. / Ng, H.Q. / Ng, E.Y. / Gea, C.Y. / Choong, M.L. / Tan, Q.W. / Koh, X. / Lim, W.H. / Nacro, K. / Cherian, J. / Baburajendran, ...Authors: Loh, Y.Y. / Anantharajan, J. / Huang, Q. / Xu, W. / Fulwood, J. / Ng, H.Q. / Ng, E.Y. / Gea, C.Y. / Choong, M.L. / Tan, Q.W. / Koh, X. / Lim, W.H. / Nacro, K. / Cherian, J. / Baburajendran, N. / Ke, Z. / Kang, C.
History
DepositionJun 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: 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)18,1724
Polymers17,8311
Non-polymers3413
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint3 kcal/mol
Surface area8260 Å2
Unit cell
Length a, b, c (Å)54.667, 54.667, 183.196
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-322-

HOH

21A-401-

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-V23 / 7-methyl-2-(trifluoromethyl)-3~{H}-[1,2,4]triazolo[1,5-a]pyridin-5-one


Mass: 217.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H6F3N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.5 M Sodium formate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→46.94 Å / Num. obs: 78895 / % possible obs: 99.95 % / Redundancy: 20 % / CC1/2: 0.994 / Net I/σ(I): 8.75
Reflection shellResolution: 1.54→1.6 Å / Num. unique obs: 4133 / CC1/2: 0.649

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→46.94 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2367 3717 4.72 %
Rwork0.2179 --
obs0.2188 78705 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1202 0 23 113 1338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131285
X-RAY DIFFRACTIONf_angle_d1.2541758
X-RAY DIFFRACTIONf_dihedral_angle_d15174
X-RAY DIFFRACTIONf_chiral_restr0.07187
X-RAY DIFFRACTIONf_plane_restr0.012229
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.560.50961270.53322601X-RAY DIFFRACTION93
1.56-1.580.53051360.51022796X-RAY DIFFRACTION100
1.58-1.60.43341390.45782764X-RAY DIFFRACTION100
1.6-1.620.42731350.42172789X-RAY DIFFRACTION100
1.62-1.650.37621390.38752815X-RAY DIFFRACTION100
1.65-1.670.40141410.35672766X-RAY DIFFRACTION100
1.67-1.70.3531340.33422782X-RAY DIFFRACTION100
1.7-1.730.30851360.30052753X-RAY DIFFRACTION100
1.73-1.760.29551370.28872854X-RAY DIFFRACTION100
1.76-1.790.31031330.26912756X-RAY DIFFRACTION100
1.79-1.830.25251390.26352775X-RAY DIFFRACTION100
1.83-1.870.31551390.27232746X-RAY DIFFRACTION100
1.87-1.910.31051400.26812795X-RAY DIFFRACTION100
1.91-1.960.31121400.2522785X-RAY DIFFRACTION100
1.96-2.010.23731390.24022799X-RAY DIFFRACTION100
2.01-2.070.30651370.2252767X-RAY DIFFRACTION100
2.07-2.140.27361400.22492793X-RAY DIFFRACTION100
2.14-2.220.22461400.2222790X-RAY DIFFRACTION100
2.22-2.310.24951350.22732760X-RAY DIFFRACTION100
2.31-2.410.26151400.23662785X-RAY DIFFRACTION100
2.41-2.540.24261410.22972798X-RAY DIFFRACTION100
2.54-2.70.24371440.22652767X-RAY DIFFRACTION100
2.7-2.90.22951360.2372795X-RAY DIFFRACTION100
2.9-3.20.32161410.21432798X-RAY DIFFRACTION100
3.2-3.660.21681350.19382780X-RAY DIFFRACTION100
3.66-4.610.15541350.14932791X-RAY DIFFRACTION100
4.61-46.940.15281390.1692788X-RAY DIFFRACTION100

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