6TD3 Ligase date Nov 07, 2019
title Structure Of Ddb1 Bound To Cr8-Engaged Cdk12-Cyclink
authors R.D.Bunker, G.Petzold, Z.Kozicka, N.H.Thoma
compound source
Molecule: Dna Damage-Binding Protein 1
Chain: A, D, G
Synonym: Ddb P127 Subunit,Dna Damage-Binding Protein A,Ddba Specific Dna-Binding Protein 1,Hbv X-Associated Protein 1,X Damaged Dna-Binding Factor,Uv-Damaged Dna-Binding Protein 1 Xpe-Binding Factor,Xpe-Bf,Xeroderma Pigmentosum Group E-Com Protein,Xpce;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddb1, Xap1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cyclin-Dependent Kinase 12
Chain: B, E, H
Synonym: Cdc2-Related Kinase,Arginineserine-Rich,Crkrs,Cel Cycle 2-Related Protein Kinase 7,Cdc2-Related Protein Kinas Division Protein Kinase 12,Hcdk12;
Ec: 2.7.11.22,2.7.11.23
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cdk12, Crk7, Crkrs, Kiaa0904
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cyclin-K
Chain: C, F, I
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ccnk, Cpr4
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
symmetry Space Group: P 31 2 1
R_factor 0.194 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
250.749 250.749 217.920 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.46 Å
ligand RC8, TPO enzyme Transferase E.C.2.7.11.22 BRENDA
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] (2862 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
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 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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