DNA ligase 3D structures

3D Structures of DNA ligase

Updated on 17-April-2025

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• ATP-dependent LigD
  • 3p4h, 3ta5, 3ta7 – LigD N-terminal – Candidatus korarchaeum cryptofilum
    
  • 3gde – LigD – Archaeoglobus fulgidus
    
  • 2hiv – SsLigD – Sulfolobus solfataricus
    
  • 2hix - SsLigD + ATP
    
  • 7rpo, 7rpw, 7rpx – SsLigD + PCNA + DNA – Cryo EM
    
  • 2cfm - LigD + AMP – Pyrococcus furiosus
    
  • 2fao - PaLigD polymerase domain – Pseudomonas aeruginosa
    
  • 2faq, 2far - PaLigD polymerase domain + ATP + Mn
    
  • 1a0i – LigD (mutant) + ATP – Bacteriophage T7
    
  • 4eq5 – LigD + AMP – Thermococcus sibiricus
    
  • 4d05 – LigD + AMP - Psychromonas
    
  • 6nhx, 6nhz – MtLigD D + ATP - Mycobacterium tuberculosis
    
  • 2iru – MtLigD D polymerase domain 1-300
    
  • 2irx, 2iry – MtLigD D polymerase domain + GTP
    
  • 3pky – MtLigD D polymerase domain + DNA + UTP
    
  • 2r9l, 4mky – MtLigD D polymerase domain + DNA
    
  • 6rar, 6ras, 6rce - PmLigD + CMP + AMP – Prochlorococcus marinus
    
  • 6rau - PmLigD + AMP
    
  • 7obn - LigD + AMP + CMP + DNA – Burkholderia pseudomallei<br />
  • 8u6x – LigE + DNA – Neisseria gonorrhoeae
    
• NAD+-dependent LigD
  • 3jsl, 3jsn - SaLigD adenylation domain – Staphylococcus aureus
    
  • 4cc5, 4cc6, 5fpo, 5fpr – SaLigD adenylation domain + inhibitor
    
  • 8jyd - EfLigD adenylation domain + NMN
  • 3ba8, 3ba9, 3baa, 3bab, 3bac, 4eeq, 4efb, 4efe, 4lh6, 4lh7 - EfLigD adenylation domain + NMN + inhibitor – Enterococcus faecalis
    
  • 1ta8, 1tae - EfLigD adenylation domain
    
  • 1zau - MtLigD adenylation domain
    
  • 3sgi, 6ksc – MtLigD A (mutant) + AMP
    
  • 7k72 – MtLigD A + AMP + NAD
    
  • 6kjm, 6krh – MtLigD A + AMP + nicotinamide ribose-MP
    
  • 6kkv, 6lw8– MtLigD A + inhibitor
    
  • 6ksd - MtLigD (mutant) + nicotinamide mononucleotide
    
  • 6kdu - MtLigD (mutant) + AMP + nicotinamide mononucleotide
    
  • 1v9p, 1dgs – LigD – Thermos filiformis
    
  • 1b04 – LigD adenylation domain (mutant) – Geobacillus stearothermophilus
    
  • 4glw – LigD A + NMN + inhibitor – Streptococcus pneumoniae
    
  • 4glx – EcLigD + DNA + inhibitor - Escherichia coli
    
  • 5tt5 - EciLigD + NAD
    
  • 3pn1, 4uco, 4ucr, 4ucs, 4uct, 4ucu, 4ucv, 4ufz – HiLigD adenylation domain + inhibitor – Haemophilus influenza
    
  • 3uq8 - HiLigD adenylation domain + NAD
    
  • 8ak4 - LigD adenylation domain – Deinococcus radiodurans
    
• LigD
  • 2q2t – CvLigD + DNA + AMP + CMP – Chlorella virus
    
  • 6imj, 6imk, 6iml, 6imn – LigD + DNA – African swine fever virus
    
  • 6gdr – LigD + DNA – Alteromonas mediterranea
    
  • 6dt1 – T4LigD + DNA – phage T4
    
  • 5wfy – T4LigD DNA-binding domain
    
  • 2q2u, 1p8l, 1fvi - CvLigD + DNA + mononucleotide
    
  • 2owo – LigD + DNA + AMP + CMP – Escherichia coli
    
  • 3qwu – LigD – Aquifex aeolicus
    
  • 1l7b – LigD BRCT domain – Thermos thermophilus - NMR
    
  • 3rr5 – LigD - Thermococcus
    
  • 6wbo - LigD + AMP – Thermococcus gammatolerans
    
  • 5frq - LigD + DNA polymerase III subunit β – Helicobacter pylori
    
• Mammalian LigD I
  • 8vds, 8vdt – hLigD I + DNA – human
  • 8vdn, 8vzl, 8vzm, 9bs3, 9bs4 – hLigD I + DNA + AMP
  • 1x9n – hLigD I + DNA + AMP + CMP
    
  • 8b8t - hLigD I + PCNA – Cryo EM
    
  • 7qnz - hLigD I + PCNA + DNA – Cryo EM
    
  • 7qo1 - hLigD I + PCNA + FEN1 + DNA – Cryo EM
    
  • 6p09, 6p0a, 6p0b, 6p0c, 6p0d, 7kr3, 7kr4, 7sx5, 7sxe, 7sum - hLigD I + DNA + AMP
    
  • 6p0e, 6q1v, 7l34, 7l35 - hLigD I (mutant) + DNA + AMP
    
  • 2od8 – LigD I residues 32-53 + PCNA
• Mammalian LigD III
  • 3l2p – hLigD III residues 257-833 + DNA
    
  • 1uw0 - hLigD III zinc-finger domain residues 1-117 – NMR
    
  • 1imo, 1in1 - hLigD III BRCT domain – NMR
    
  • 3pc7 - hLigD III BRCT domain 932-1009
    
  • 3qvg - hLigD III BRCT domain + XRCC1
    
  • 3pc8 - hLigD III BRCT domain (mutant) + XRCC1
    
• Mammalian LigD IV; Domains - catalytic 1-609; DNA-binding 1-240;adenylation 268-405; BRCT 654-911
  • 3w5o - hLigD IV catalytic domain
    
  • 3ii6, 1ik9 – hLigD IV C-terminal BRCT domains + DNA repair protein XRCC4
    
  • 2e2w - hLigD IV BRCT domain 654-759 - NMR
    
  • 3vnn - hLigD IV adenylation domain
    
  • 4hto, 7d9k - hLigD IV DNA-binding domain
    
  • 7d9y - hLigD IV DNA-binding domain (mutant)
    
  • 4htp - hLigD IV DNA-binding domain + artemis protein peptide
    
  • 3w1b, 3w1g - hLigD IV adenylation and DNA-binding domains + artemis protein peptide
    
  • 6bkg, 6bkf - hLigD IV catalytic domain + DNA + AMP
    
  • 7lsy, 7lt3, 7nfc, 7nfe, 8eza, 8ezb - hLigD IV in NHEJ short-range synaptic complex – Cryo EM
    
  • 1z56 – LigD IV + ligase interacting factor 1 - yeast
    

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Michal Harel, Jaime Prilusky