Exonuclease 3D structures

3D Structures of exonuclease

Updated on 04-June-2025

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• ExN-I
  • 3qea, 3qeb, 5v04, 5v05, 5v06, 5v0b, 5v0c, 5v0d, 5v0e, 5uzv - hExN-I + DNA - human
    
  • 3qe9, 5v07, 5v08, 5v09, 5v0a – hExN-I (mutant) + DNA
    
  • 5fiq, 5fis – ExN-I ExN domain – silkworm
    
  • 1fxx, 3c95 – EcExN-I – Escherichia coli
    
  • 2qxf - EcExN-I + TMP
    
  • 3hl8, 3hp9 - EcExN-I + inhibitor
    
  • 3c94 - EcExN-I + DNA-binding C terminal peptide
    
  • 4jrp, 4jrq, 4js5, 4js4, 4hcc, 4hcb – EcExN-I + DNA
    
  • 4rg8 – ExN-I (mutant) – Methylocaldum szegedienes
    
• ExN-III
  • 2voa – AfExN-III (mutant) + DNA – Archaeoglobus fulgidus
    
  • 3g1k - MtExN-III – Methanothermobacter thermaautotrophicus
    
  • 3g3c, 3g4t - MtExN-III + DNA
    
  • 3fzi, 3g8v, 3g91 - MtExN-III (mutant)
    
  • 3g00, 3g0r, 3g2c, 3g2d, 3g38, 3g3y, 3ga6 - MtExN-III (mutant) + DNA
    
  • 3g0a - MtExN-III (mutant) + Mn
    
  • 1ako – EcExN-III
• ExN-IV
  • 2jc4 – ExN-IV – Nisseria meningitides
• ExN-V or RecBCD
  • 7lw7 – hExN-V (mutant)
    
  • 7lw8, 7lw9, 7lwa – hExN-V (mutant) + DNA – Cryo EM
    
  • 3e1s - EcExN-V RecD subunit
    
  • 1w36, 3k70 – EcExN-V RecB+RecC+RecD subunits + DNA hairpin
    
  • 5ld2 – EcExN-V RecB+RecC+RecD subunits + DNA – Cryo EM
    
  • 5mbv – EcExN-V RecB+RecC+RecD subunits + GAMS – Cryo EM
    
  • 6sjb, 6sje, 6sjf, 6sjg, 6t2u, 6t2v – EcExN-V RecB (mutant)+RecC+RecD subunits + DNA – Cryo EM
    
  • 3gp8 - DrExN-V RecD subunit + DNA – Deinococcus radiodurans
    
  • 3gpl - DrExN-V RecD subunit + DNA + ADPNP
• ExN-VII
  • 1vp7 – ExN-VII small subunit – Bordetella pertussis
• ExN-VIII
  • 3h4r - EcExN-VIII C terminal (mutant)
• ExN-X
  • 4fzz, 4fzy, 4fzx - EcExN-X + DNA
    
• 5’ ExN or exodeoxyribonuclease
  • 1ut5, 1ut8 – T5-5’-ExN + metal – Bacteriophage T5
    
  • 1exn, 1xo1 - T5-5’-ExN (mutant)
    
  • 5hmm - EpT5-5’-ExN + metal – Escherichia phage T5
    
  • 5hml - EpT5-5’-ExN (mutant) + metal
    
  • 5hnk, 5hp4 - EpT5-5’-ExN (mutant) + metal + DNA
    
  • 1avq – BlExN λ (mutant) – Bacteriophage λ
    
  • 3slp, 4wuz - BlExN λ + DNA
    
  • 3sm4 - BlExN λ (mutant) + DNA
    
  • 6lpm - Dr5’-ExN III
    
  • 3k93 – ExN – Haemophilus somnus
• Exosome complex ExN see Exosome
• ssDNA-specific ExN
  • 5ght – TkExN – Thermococcus kodakarensis
    
  • 5ghs, 5ghr – TkExN + polypeptide
    
  • 7e15 – TkExN + GINS51 + DNA polymerase II small subunit
    
  • 5f54 – DrExN + dTMP
    
  • 5f55 – DrExN + DNA
    
  • 5f56 – DrExN + DNA + polypeptide
    
• 3'-5' ExN
  • 4qoz, 4l8r – hExN + histone RNA hairpin-binding protein + RNA
    
  • 8zef – hExN DING + DNA
    
  • 8q1k, 8q1x, 8s86 – hExN PLD3
    
  • 8v08 – hExN PLD4 + ssDNA
    
  • 8v05, 8v07, 8v5t – mExN PLD3
    
  • 8v06 – mExN PLD3 + ssDNA
    
  • 4yor, 4yot, 4you – PhExN phoexo I – Pyrococcus horikoshii
    
  • 4yov, 4yow, 4yox, 4yoy – PhExN phoexo I (mutant) + DNA
    
  • 7t2s – EcExN
    
  • 9f7l – ExN + pGG – Bartonella henselae
    
• 3’-5’ ExN oligoribonuclease (ORN)
  • 3tr8 – ORN – Coxiella burnetii
    
  • 5cy4 – ORN – Acinetobacter baumannii
    
  • 6a4a – CpORN – Colwella psychrerythraea
    
  • 6a4d – CpORN (mutant) + PNP-TMP
    
  • 6a4e – CpORN (mutant) + RNA
    
  • 6a4f – CpORN + UMP
    
  • 2gbz – ORN – Xanthomonas campestris
    
  • 1yta, 2igi – EcORN
    
  • 1j9a – ORN – Haemophilus influenzae
    
  • 6n6a, 6n6c, 6n6d, 6n6e 6n6f, 6n6g, 6n6h – ORN + RNA – Vibrio cholerae
    
• 5’-3’ ExN
  • 6c33 – MsExN – Mycobacterium smegmatis
    
  • 6c34, 6c35, 6c36 – MsExN (mutant)
    
• ExN Trex or three-prime repair exonuclease 1
  • 7tqn, 7tqo, 7tqp - hExN Trex1 (mutant)
    
  • 7tqq - hExN Trex1 + DNA
    
  • 8vl7, 9ava, 9o0w, 9o0x, 9o0y - hExN Trex1 + inhibitor
    
  • 1y97 – hExN Trex2
    
  • 2o4g - mExN Trex1 + nucleotide – mouse
    
  • 2ioc, 3mxj - mExN Trex1
    
  • 6w10 - mExN Trex1 (mutant)
    
  • 2o4i, 3mxi, 3mxm, 3u3y, 3u6f - mExN Trex1 (mutant) + polynucleotide
    
  • 2oa8, 5ywv, 5ywu, 5ywt, 5yws - mExN Trex1 + DNA
    
  • 8hcc, 8hcd, 8hce, 8hcf - mExN Trex1 + nucleotide
  • 4ynq - mExN Trex1 (mutant) + DNA
    

3b6o, 3b6p - mExN Trex1 + ion inhibitor

• • 7u8y - mExN Trex1 + inhibitor
    
  • 8hch - mExN Trex1 + uridine
    
  • 3b6o, 3b6p - mExN Trex1 + ion inhibitor
    
  • 6a45 - mExN Trex2
    
  • 6a4b, 6a47 - mExN Trex2 + DNA
    
  • 6a46 - mExN Trex2 + nucleotide
    
• RNA ExN homolog or oligoribonuclease or REXO2
  • 6rci – hExN2
    
  • 6j7y – hExN2 + DNA
    
  • 6j80, 6rcn – hExN2 (mutant) + DNA
    
  • 6n6i, 6n6j, 6n6k, 6rcl, 6sty – hExN2 + RNA
    
  • 6j7z – hExN2 (mutant) + RNA
    
• Other ExN
  • 1w0h – hExn Eri1 nuclease domain
    
  • 1zbu - hExn Eri1
    
  • 1zbh - hExn Eri1 (mutant) + DNA
    
  • 5aho, 7b9b – hExN Apollo
    
  • 7b2x – hExN Apollo (mutant)
    
  • 7a1f – hExN Apollo + AMP
    
  • 5zyw – hExN mitochondrial genome repair 1
    
  • 5zyv, 5zyu, 5zyt – hExN mitochondrial genome repair 1 + DNA
    
  • 8q66 – ExN Mut-7 + SH2 domain-containing protein – Caenorhabditis elegans
    
  • 3e2v – yExN
    
  • 2w45 – H4ExN alkaline - Herpesvirus 4
    
  • 2w4b - H4ExN alkaline (mutant)
    
  • 3syy - LhExN alkaline – Laribacter hongkongensis
    
  • 3sz4 - LhExN alkaline + AMP
    
  • 3sz5 - LhExN alkaline + polynucleotide
    
  • 4lty, 4lu9, 4m0v – EcExN sbcD
    
  • 6m9k - ExN + recombination protein BET – Escherichia phage λ
    
  • 1ir6, 2zxo, 2zxp, 2zxr – ExN Recj – Thermus thermophiles
    
  • 8y30 - ExN Recj – Staphylococcus aureus

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Michal Harel