DNA ligase 3D structures
From Proteopedia
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**[[2hiv]] – SsLigD – ''Sulfolobus solfataricus''<br /> | **[[2hiv]] – SsLigD – ''Sulfolobus solfataricus''<br /> | ||
**[[2hix]] - SsLigD + ATP<br /> | **[[2hix]] - SsLigD + ATP<br /> | ||
| + | **[[7rpo]], [[7rpw]], [[7rpx]] – SsLigD + PCNA + DNA – Cryo EM<br /> | ||
**[[2cfm]] - LigD + AMP – ''Pyrococcus furiosus''<br /> | **[[2cfm]] - LigD + AMP – ''Pyrococcus furiosus''<br /> | ||
**[[2fao]] - PaLigD polymerase domain – ''Pseudomonas aeruginosa''<br /> | **[[2fao]] - PaLigD polymerase domain – ''Pseudomonas aeruginosa''<br /> | ||
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**[[4d05]] – LigD + AMP - ''Psychromonas'' <br /> | **[[4d05]] – LigD + AMP - ''Psychromonas'' <br /> | ||
**[[6nhx]], [[6nhz]] – MtLigD D + ATP - ''Mycobacterium tuberculosis'' <br /> | **[[6nhx]], [[6nhz]] – MtLigD D + ATP - ''Mycobacterium tuberculosis'' <br /> | ||
| + | **[[2iru]] – MtLigD D polymerase domain 1-300 <br /> | ||
| + | **[[2irx]], [[2iry]] – MtLigD D polymerase domain + GTP <br /> | ||
| + | **[[3pky]] – MtLigD D polymerase domain + DNA + UTP <br /> | ||
| + | **[[2r9l]], [[4mky]] – MtLigD D polymerase domain + DNA <br /> | ||
**[[6rar]], [[6ras]], [[6rce]] - PmLigD + CMP + AMP – ''Prochlorococcus marinus''<br /> | **[[6rar]], [[6ras]], [[6rce]] - PmLigD + CMP + AMP – ''Prochlorococcus marinus''<br /> | ||
**[[6rau]] - PmLigD + AMP <br /> | **[[6rau]] - PmLigD + AMP <br /> | ||
| + | **[[7obn]] - LigD + AMP + CMP + DNA – ''Burkholderia pseudomallei<''br /> | ||
| + | **[[8u6x]] – LigE + DNA – ''Neisseria gonorrhoeae''<br /> | ||
*NAD+-dependent LigD | *NAD+-dependent LigD | ||
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**[[3jsl]], [[3jsn]] - SaLigD adenylation domain – ''Staphylococcus aureus''<br /> | **[[3jsl]], [[3jsn]] - SaLigD adenylation domain – ''Staphylococcus aureus''<br /> | ||
**[[4cc5]], [[4cc6]], [[5fpo]], [[5fpr]] – SaLigD adenylation domain + inhibitor <br /> | **[[4cc5]], [[4cc6]], [[5fpo]], [[5fpr]] – SaLigD adenylation domain + inhibitor <br /> | ||
| + | **[[8jyd]] - EfLigD adenylation domain + NMN | ||
**[[3ba8]], [[3ba9]], [[3baa]], [[3bab]], [[3bac]], [[4eeq]], [[4efb]], [[4efe]], [[4lh6]], [[4lh7]] - EfLigD adenylation domain + NMN + inhibitor – ''Enterococcus faecalis''<br /> | **[[3ba8]], [[3ba9]], [[3baa]], [[3bab]], [[3bac]], [[4eeq]], [[4efb]], [[4efe]], [[4lh6]], [[4lh7]] - EfLigD adenylation domain + NMN + inhibitor – ''Enterococcus faecalis''<br /> | ||
**[[1ta8]], [[1tae]] - EfLigD adenylation domain<br /> | **[[1ta8]], [[1tae]] - EfLigD adenylation domain<br /> | ||
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**[[6kjm]], [[6krh]] – MtLigD A + AMP + nicotinamide ribose-MP<br /> | **[[6kjm]], [[6krh]] – MtLigD A + AMP + nicotinamide ribose-MP<br /> | ||
**[[6kkv]], [[6lw8]]– MtLigD A + inhibitor<br /> | **[[6kkv]], [[6lw8]]– MtLigD A + inhibitor<br /> | ||
| + | **[[6ksd]] - MtLigD (mutant) + nicotinamide mononucleotide<br /> | ||
**[[6kdu]] - MtLigD (mutant) + AMP + nicotinamide mononucleotide<br /> | **[[6kdu]] - MtLigD (mutant) + AMP + nicotinamide mononucleotide<br /> | ||
**[[1v9p]], [[1dgs]] – LigD – ''Thermos filiformis''<br /> | **[[1v9p]], [[1dgs]] – LigD – ''Thermos filiformis''<br /> | ||
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**[[4glx]] – EcLigD + DNA + inhibitor - ''Escherichia coli''<br /> | **[[4glx]] – EcLigD + DNA + inhibitor - ''Escherichia coli''<br /> | ||
**[[5tt5]] - EciLigD + NAD<br /> | **[[5tt5]] - EciLigD + NAD<br /> | ||
| - | **[[3pn1]], [[4uco]], [[4ucr]], [[4ucs]], [[4uct]], [[4ucu]], [[4ucv]], [[4ufz]] – HiLigD adenylation domain + inhibitor – Haemophilus influenza<br /> | + | **[[3pn1]], [[4uco]], [[4ucr]], [[4ucs]], [[4uct]], [[4ucu]], [[4ucv]], [[4ufz]] – HiLigD adenylation domain + inhibitor – ''Haemophilus influenza''<br /> |
**[[3uq8]] - HiLigD adenylation domain + NAD<br /> | **[[3uq8]] - HiLigD adenylation domain + NAD<br /> | ||
| + | **[[8ak4]] - LigD adenylation domain – ''Deinococcus radiodurans''<br /> | ||
*LigD | *LigD | ||
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*Mammalian LigD I | *Mammalian LigD I | ||
| - | **[[1x9n]] – hLigD I + DNA + AMP + CMP – | + | **[[8vds]], [[8vdt]] – hLigD I + DNA – human |
| - | **[[6p09]], [[6p0a]], [[6p0b]], [[6p0c]], [[6p0d]], [[7kr3]], [[7kr4]] - hLigD I + DNA + AMP<br /> | + | **[[8vdn]], [[8vzl]], [[8vzm]], [[9bs3]], [[9bs4]] – hLigD I + DNA + AMP |
| + | **[[1x9n]] – hLigD I + DNA + AMP + CMP <br /> | ||
| + | **[[8b8t]] - hLigD I + PCNA – Cryo EM<br /> | ||
| + | **[[7qnz]] - hLigD I + PCNA + DNA – Cryo EM<br /> | ||
| + | **[[7qo1]] - hLigD I + PCNA + FEN1 + DNA – Cryo EM<br /> | ||
| + | **[[6p09]], [[6p0a]], [[6p0b]], [[6p0c]], [[6p0d]], [[7kr3]], [[7kr4]], [[7sx5]], [[7sxe]], [[7sum]] - hLigD I + DNA + AMP<br /> | ||
**[[6p0e]], [[6q1v]], [[7l34]], [[7l35]] - hLigD I (mutant) + DNA + AMP<br /> | **[[6p0e]], [[6q1v]], [[7l34]], [[7l35]] - hLigD I (mutant) + DNA + AMP<br /> | ||
**[[2od8]] – LigD I residues 32-53 + PCNA | **[[2od8]] – LigD I residues 32-53 + PCNA | ||
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**[[3pc8]] - hLigD III BRCT domain (mutant) + XRCC1<br /> | **[[3pc8]] - hLigD III BRCT domain (mutant) + XRCC1<br /> | ||
| - | *Mammalian LigD IV; Domains - catalytic 1-609; DNA-binding 1-240; adenylation 268-405; BRCT 654-911 | + | *Mammalian LigD IV; Domains - catalytic 1-609; DNA-binding 1-240;adenylation 268-405; BRCT 654-911 |
**[[3w5o]] - hLigD IV catalytic domain <br /> | **[[3w5o]] - hLigD IV catalytic domain <br /> | ||
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**[[3w1b]], [[3w1g]] - hLigD IV adenylation and DNA-binding domains + artemis protein peptide<br /> | **[[3w1b]], [[3w1g]] - hLigD IV adenylation and DNA-binding domains + artemis protein peptide<br /> | ||
**[[6bkg]], [[6bkf]] - hLigD IV catalytic domain + DNA + AMP<br /> | **[[6bkg]], [[6bkf]] - hLigD IV catalytic domain + DNA + AMP<br /> | ||
| - | **[[7lsy]], [[7lt3]] - hLigD IV in NHEJ short-range synaptic complex – Cryo EM<br /> | + | **[[7lsy]], [[7lt3]], [[7nfc]], [[7nfe]], [[8eza]], [[8ezb]] - hLigD IV in NHEJ short-range synaptic complex – Cryo EM<br /> |
**[[1z56]] – LigD IV + ligase interacting factor 1 - yeast<br /> | **[[1z56]] – LigD IV + ligase interacting factor 1 - yeast<br /> | ||
Current revision
3D Structures of DNA ligase
Updated on 17-April-2025
