DNA ligase 3D structures

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Line 10: Line 10:
**[[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 />
Line 17: Line 18:
**[[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
Line 24: Line 31:
**[[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 />
**[[1zau]] - MtLigD adenylation domain <br />
**[[1zau]] - MtLigD adenylation domain <br />
-
**[[3sgi]] – MtLigD (mutant) + AMP<br />
+
**[[3sgi]], [[6ksc]] – MtLigD A (mutant) + AMP<br />
 +
**[[7k72]] – MtLigD A + AMP + NAD<br />
 +
**[[6kjm]], [[6krh]] – MtLigD A + AMP + nicotinamide ribose-MP<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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**[[1l7b]] – LigD BRCT domain – ''Thermos thermophilus'' - NMR<br />
**[[1l7b]] – LigD BRCT domain – ''Thermos thermophilus'' - NMR<br />
**[[3rr5]] – LigD - ''Thermococcus''<br />
**[[3rr5]] – LigD - ''Thermococcus''<br />
 +
**[[6wbo]] - LigD + AMP – ''Thermococcus gammatolerans''<br />
**[[5frq]] - LigD + DNA polymerase III subunit β – ''Helicobacter pylori''<br />
**[[5frq]] - LigD + DNA polymerase III subunit β – ''Helicobacter pylori''<br />
*Mammalian LigD I
*Mammalian LigD I
-
**[[1x9n]] – hLigD I + DNA + AMP + CMP – human<br />
+
**[[8vds]], [[8vdt]] – hLigD I + DNA – human
-
**[[6p09]], [[6p0a]], [[6p0b]], [[6p0c]], [[6p0d]] - hLigD I + DNA + AMP<br />
+
**[[8vdn]], [[8vzl]], [[8vzm]], [[9bs3]], [[9bs4]] – hLigD I + DNA + AMP
-
**[[6p0e]], [[6q1v]] - hLigD I (mutant) + DNA + AMP<br />
+
**[[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 />
**[[2od8]] – LigD I residues 32-53 + PCNA
**[[2od8]] – LigD I residues 32-53 + PCNA
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**[[3l2p]] – hLigD III residues 257-833 + DNA<br />
**[[3l2p]] – hLigD III residues 257-833 + DNA<br />
**[[1uw0]] - hLigD III zinc-finger domain residues 1-117 – NMR<br />
**[[1uw0]] - hLigD III zinc-finger domain residues 1-117 – NMR<br />
-
**[[1imo]], [[1in1]] - hLigD III BRCTdomain – NMR<br />
+
**[[1imo]], [[1in1]] - hLigD III BRCT domain – NMR<br />
-
**[[3pc7]] - hLigD III BRCTdomain<br />
+
**[[3pc7]] - hLigD III BRCT domain 932-1009<br />
-
**[[3pc8]] - hLigD III BRCTdomain (mutant) + XRCC1<br />
+
**[[3qvg]] - hLigD III BRCT domain + XRCC1<br />
-
**[[3qvg]] - hLigD III BRCTdomain + XRCC1
+
**[[3pc8]] - hLigD III BRCT domain (mutant) + XRCC1<br />
-
*Mammalian LigD IV
+
*Mammalian LigD IV; Domains - catalytic 1-609; DNA-binding 1-240;adenylation 268-405; BRCT 654-911
-
**[[3ii6]], [[ 1ik9]] – hLigD IV C-terminal BRCT domains + DNA repair protein XRCC4<br />
+
**[[3w5o]] - hLigD IV catalytic domain <br />
-
**[[3w5o]] - hLigD IV <br />
+
**[[3ii6]], [[1ik9]] – hLigD IV C-terminal BRCT domains + DNA repair protein XRCC4<br />
-
**[[2e2w]] - hLigD IV BRCT domain - NMR<br />
+
**[[2e2w]] - hLigD IV BRCT domain 654-759 - NMR<br />
-
**[[3vnn]] - hLigD IV adenylation domain<br />
+
**[[3vnn]] - hLigD IV adenylation domain <br />
-
**[[4hto]] - hLigD IV DNA-binding domain<br />
+
**[[4hto]], [[7d9k]] - hLigD IV DNA-binding domain <br />
 +
**[[7d9y]] - hLigD IV DNA-binding domain (mutant)<br />
**[[4htp]] - hLigD IV DNA-binding domain + artemis protein peptide<br />
**[[4htp]] - hLigD IV DNA-binding domain + artemis protein peptide<br />
**[[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 + DNA<br />
+
**[[6bkg]], [[6bkf]] - hLigD IV catalytic domain + DNA + AMP<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

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel

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