6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK date
authors Bunker, R.D., Petzold, G., Kozicka, Z., Thoma, N.H.
compound source
symmetry
R_factor
R_Free 0.22
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.46
ligand RC8, TPO enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, G


E, B, H


F, C, I


Primary referenceThe CDK inhibitor CR8 acts as a molecular glue degrader that depletes cyclin K., Slabicki M, Kozicka Z, Petzold G, Li YD, Manojkumar M, Bunker RD, Donovan KA, Sievers QL, Koeppel J, Suchyta D, Sperling AS, Fink EC, Gasser JA, Wang LR, Corsello SM, Sellar RS, Jan M, Gillingham D, Scholl C, Frohling S, Golub TR, Fischer ES, Thoma NH, Ebert BL, Nature. 2020 Jun 3. pii: 10.1038/s41586-020-2374-x. doi:, 10.1038/s41586-020-2374-x. PMID:32494016
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2930 Kb) [Save to disk]
  • Biological Unit Coordinates (6td3.pdb1.gz) 953 Kb
  • Biological Unit Coordinates (6td3.pdb2.gz) 960 Kb
  • Biological Unit Coordinates (6td3.pdb3.gz) 954 Kb
  • LPC: Ligand-Protein Contacts for 6TD3
  • CSU: Contacts of Structural Units for 6TD3
  • Structure Factors (3301 Kb)
  • Retrieve 6TD3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6TD3 from S2C, [Save to disk]
    • View 6TD3 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 6TD3
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6td3 from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6td3_I] [6td3_E] [6td3_C] [6td3_D] [6td3_G] [6td3_H] [6td3_A] [6td3_F] [6td3_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6TD3
  • Community annotation for 6TD3 at PDBWiki (http://pdbwiki.org)

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