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

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Basic information

Entry
Database: PDB / ID: 8jvd
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 / 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
: / Ubiquitin-conjugating enzyme E2 T
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 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 28, 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)17,9832
Polymers17,8311
Non-polymers1521
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8320 Å2
Unit cell
Length a, b, c (Å)54.636, 54.636, 182.728
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-321-

HOH

21A-396-

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-V2R / 5-fluoranyl-1,3-benzoxazol-2-amine


Mass: 152.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5FN2O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 3.5M 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: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.69→46.891 Å / Num. obs: 31816 / % possible obs: 99.8 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.011 / Rrim(I) all: 0.057 / Χ2: 0.53 / Net I/σ(I): 23.5
Reflection shellResolution: 1.7→1.73 Å / % possible obs: 96.2 % / Redundancy: 24.5 % / Rmerge(I) obs: 1.461 / Num. measured all: 38385 / Num. unique obs: 1569 / CC1/2: 0.916 / Rpim(I) all: 0.296 / Rrim(I) all: 0.01492 / Χ2: 0.43 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.696→46.891 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1996 6.31 %
Rwork0.2276 --
obs0.2293 31637 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.696→46.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 11 99 1328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131291
X-RAY DIFFRACTIONf_angle_d1.2421766
X-RAY DIFFRACTIONf_dihedral_angle_d8.2841106
X-RAY DIFFRACTIONf_chiral_restr0.074188
X-RAY DIFFRACTIONf_plane_restr0.01232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.696-1.73830.37371360.34362014X-RAY DIFFRACTION99
1.7383-1.78530.40281390.322077X-RAY DIFFRACTION100
1.7853-1.83790.3671410.30532074X-RAY DIFFRACTION99
1.8379-1.89720.34821370.28162067X-RAY DIFFRACTION99
1.8972-1.9650.32891410.27452090X-RAY DIFFRACTION100
1.965-2.04370.29411410.26482074X-RAY DIFFRACTION100
2.0437-2.13670.28521410.2512096X-RAY DIFFRACTION100
2.1367-2.24930.27111400.24742083X-RAY DIFFRACTION99
2.2493-2.39030.31681430.25732114X-RAY DIFFRACTION100
2.3903-2.57480.30031440.26892125X-RAY DIFFRACTION100
2.5748-2.83390.25941420.26822130X-RAY DIFFRACTION100
2.8339-3.24390.28531460.25742160X-RAY DIFFRACTION100
3.2439-4.08660.21411470.20022194X-RAY DIFFRACTION100
4.0866-46.890.2111580.1762343X-RAY DIFFRACTION100

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