DNA damage-binding protein 3D structures

3D Structures of DNA damage-binding protein

Updated on 16-April-2025

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• DDB1
  • 3e0c – hDDB - human
    
  • 2b5m, 2b5n – hDDB BPB domain
    
• DDB1 binary complex
  • 2b5l – hDDB + simian virus 5 protein
    
  • 3i7h, 3i7k, 3i7l, 3i7n, 3i7o, 3i7p, 3i89, 3i8c, **3i8e – hDDB + X protein peptide
    
  • 6dsz – hDDB + DET1 peptide
    
  • 4a11, 6fcv – hDDB + DNA excision repair protein ERCC-8
    
  • 8d7x, 8d7y – hDDB + cereblon
    
  • 8cvp – hDDB + cereblon – Cryo EM
    
  • 6zue – hDDB + DCAF1
    
  • 8ajn – hDDB + DCAF1 – Cryo EM
    
  • 7ukn – hDDB + herpes virus protein br />
  • 7v7b – hDDB + VPRBP – Cryo EM
    
  • [8wqr]] – hDDB + AMBRA1 E3 ligase receptor – Cryo EM
    
  • 9bbe, 9bbg, 9bbh, 9bbi – hDDB + indole derivative
    
• DDB1 ternary complex
  • 4ci1, 4ci2, 4ci3, 4tz4, 8d81, 8oiz, 9fjx – hDDB + cereblon + thalidomide derivative
    
  • 5v3o, 8ojh – hDDB + cereblon + piperidine derivative
    
  • 5fqd – hDDB + cereblon + casein kinase 1
    
  • 5hxb, 6xk9 – hDDB + cereblon + ERF3A
    
  • 6bn8, 6bn9, 6bnb, 6boy – hDDB + cereblon + BRD4
    
  • 7lps – hDDB + cereblon + IKAROS
    
  • 8d7u, 8d7v, 8d7w – hDDB + cereblon + mezigdomide
    
  • 6h0f – hDDB (mutant) + cereblon + IKAROS
    
  • 6h0g – hDDB (mutant) + cereblon + ZNF692
    
  • 6td3, 8bu1, 8bu2, 8bu3, 8bu4, 8bu5, 8bu6, [8bu7]], 8bu9, 8bua, 8bub, 8buc, 8bud, 8bue, 8buf, 8bug, 8buh, 8bui, 8buj, 8buk, 8bul, 8bum, 8bun, 8buo, 8bup, 8buq, 8bur, 8bus, 8but – hDDB + cyclin-dependent kinase 12 + cyclin-K
    
  • 7zn7, 7znn – hDDB (mutant) + herpes virus protein + STAT2 – Cryo EM
    
  • 6zx9 – hDDB + SIV protein + VPRBP
    
  • 8ajm, 8ajo – hDDB + DCAF1 + CCT5 – Cryo EM
    
  • 8tl6 – hDDB + DCAF5 + DDA1 – Cryo EM
    
  • 8t9a – hDDB + DCAF12 + Magea3 – Cryo EM
    
  • 9dhd – hDDB + Det-1 + DDA1 – Cryo EM
    
• DDB1 quaternary complex
  • 6uml – hDDB + cereblon + ZNF797 + thalidomide derivative
    
  • 6bn7 – hDDB + cereblon + BRD4 + piperidine derivative
    
  • 8tzx – hDDB + cereblon + WIZ + piperidine derivative
    
  • 7u8f, 8dey – hDDB + cereblon + ikzf2 + molecular gluebr />
  • 8tnq, 8tnr – hDDB + cereblon + SD40 + piperidine derivative – Cryo EM
    
  • 8g66 – hDDB + cereblon + kasein kinase + piperidine derivative – Cryo EM
    
  • 8uh6 – hDDB + cereblon + TCPTP + piperidine derivative – Cryo EM
    
  • 8tnp – hDDB + cereblon + SD40 + thalidomide derivative – Cryo EM
    
  • 8u16, 8u17 – hDDB + cereblon + Sall4 + thalidomide derivative – Cryo EM
    
  • 9bjz – hDDB + UBCH8 + Det-1 + DDA1 – Cryo EM
    
  • 8qh5 – hDDB + CSA + UVSSA + DDA1 – Cryo EM
    
  • 8g46 – hDDB + DCAF16 + DDA1 + BRD4 + MMH2– Cryo EM
    
  • 8d7z, 8d80 – hDDB + cereblon + IKAROS + drug
    
  • 2hye – hDDB + simian virus 5 protein + cullin-4A + RBX1
    
  • 5jk7 – hDDB + HIV protein + uracil-DNA glycosylase + VPRBP
    
  • 7v7c – hDDB + HIV protein + uracil-DNA glycosylase + VPRBP – Cryo EM
    
  • 7okq – hDDB + DCAF1 + cullin-4A + RBX1 – Cryo EM
    
  • 6pai, 6q0r, 6ue5 – hDDB + DDA1 + RNA-binding protein 39 + DET1 + sulfonamide derivative
    
  • 6q0v, 6q0w, 6ud7 – hDDB + DDA1 + RNA-binding protein 39 + Det-1 + anti-cancer drug
    
  • 6sj7 – hDDB + DDA1 + RNA-binding protein 39 + Det-1 + anti-cancer drug – Cryo EM
    
  • 9fmr – hDDB + cyclin-dependent kinase 12 + cyclin-K + molecular glue
    
  • 7oo3, 7oob, 7oop, 7opc, 7opd, 9bz0 – hDDB in transcription-DNA repair coupling – Cryo EM
    
  • 8b3d, 8b3f, 8b3g, 8b3i, 9bz0, 9er2, 9fd2 – hDDB in RNA polymerase II complex – Cryo EM
    
• DDB1+DDB2
  • 3ei3, 3ei4 – hDDB
    
  • 3ei1, 3ei2, 4a08, 4a09, 4a0a, 4a0b, 4e54, 4e5z – hDDB + DNA
    
  • 4a0k – hDDB + cullin-4A + ring-box protein 1
    
  • 4a0l – hDDB + cullin-4A + ring-box protein 1 + DNA
    
  • 6r8y, 6r8z, 6r90, 6r91, 6r92 – hDDB + histones + DNA – Cryo EM
    

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Michal Harel