Virus protease 3D structures

Updated on 29-March-2026 - For a general description of the protein see Virus protease

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• HIV-1 protease . See Immunodeficiency virus protease
• HIV-2 protease See Immunodeficiency virus protease
• Feline Immunodeficiency virus protease See Immunodeficiency virus protease
• Simian Immunodeficiency virus protease See Immunodeficiency virus protease
• Xenotropic murine leukemia virus protease
  • 3nr6 – XMRV-PR P14
    
  • 3p1g – XMRV-PR RNase H domain (mutant)
    
  • 3slz – XMRV-PR residues 533-657 + inhibitor
    
  • 3sm1 – XMRV-PR residues 533-657 + pepstatin
    
  • 3sm2 – XMRV-PR residues 533-657 + amprenavir
    
• Human T-cell leukemia virus protease
  • 2b7f – HTLV-PV + peptide
    
  • 3lin, 3liq, 3lit, 3liv, 3lix, 3liy, 3wsj, 4ydg, 4ydf – HTLV-PV (mutant) + inhibitor
    
• Rous sarcoma virus protease
  • 2rsp – RSVP - Rous sarcoma virus
    
  • 1bai – RSVP + polypeptide inhibitor
• Human Cytomegalovirus or (human betaherpesvirus 5) protease
  • 1wpo – CMVP
    
  • 1cmv, 1lay, 1jq6, 1id4, 1iec, 1ied, 1ief, 1ieg – CMVP (mutant)
    
  • 2wpo, 1jq7 - CMVP (mutant) + inhibitor
    
  • 1njt, 1nju, 1nkk, 1nkm - CMVP (mutant) + peptide inhibitor
    
• Varicella-Zoster virus protease
  • 1vzv - VZVP (mutant) – human alphaherpesvirus 3
• Equine infectious anemia virus protease
  • 2fmb, 1fmb – EIAVP (mutant) + inhibitor
• Hepatitis A virus protease
  • 1hav – HAVP (mutant) – hepatitis A virus
    
  • 2h9h, 2hal – HAVP residues 1520-1731 (mutant) + polypeptide inhibitor
    
  • 2h6m – HAVP + peptide inhibitor
    
  • 1qa7, 3r0f – HAVP (mutant) + inhibitor
    
• Hepatitis C virus protease
  • 1a1r, 1jxp, 1ns3, 3kf2, 3rc6, 4b6e, 4b6f – HCVP NS3/A4
    
  • 2o8m, 2oin, 4b71, 4b73, 4b74, 4b75, 4b76, 6vdn, 6vdo – HCVP (mutant)
    
  • 1bt7 – HCVP NS3 N terminal - NMR
    
  • 1w3c, 2a4g, 2gvf, 2f9u, 2f9v, 3m5m, 3m5n, 3m5o, 3oyp, 4a1t, 4a1v, 4a1x, 4jmy – HCVP + peptide inhibitor
    
  • 1dxp, 1dy8, 1dy9, 1rtl, 2a4g, 2a4q, 2f9u, 2f9v, 2fm2, 2gvf, 2obo, 2oc1, 2oc7, 2oc8, 2xcf, 2xcn, 2xni, 3eyd, 3kee, 3kn2, 3knx, 3m5l, 3lon, 3p8n, 3p8o, 3sud, 4a92, 4i31, 4k8b, 4ktc, 4nwl, 4tyd, 4u01, 4wxp, 5eqq, 5fpy, 5voj, 5vp9, 6cvw, 6cvx, 6cvy, 6diq, 6dir, 6dis, 6dit, 6diu, 6nzv, 7d5l – HCVP NS3/A4 + inhibitor
    
  • 6pj2 – HCVP NS3/A4 (mutant) + inhibitor - NMR
    
  • 3sue, 3suf, 3sug, 4i32, 4i33, 5epn, 5epy, 5etx, 6c2m, 6div, 6diw, 6nzt, 6nzv, 6piu, 6piv, 6piw, 6pix, 6piy, 6piz, 6pj0 – HCVP NS3/A4 (mutant) + inhibitor
    
  • 1a1q, 5wdx – HCVP NS3
    
  • 2oc0, 3r7b, 4nwk, 4ojq, 4ok3, 4ok5, 4ok6, 4oks, 4wxr, 5fps, 5fpt – HCVP NS3 + inhibitor
    
  • 2k1q, 6fe6 – HCVP NS3 + inhibitor - NMR
    
  • 5e4f – HCVP NS3 + ADP
    
  • 3kql, 3kqn, 3kqu – HCVP NS3 + RNA
    
  • 2f55 – HCVP NS3 + DNA
    
  • 3lox, 3su3, 3sv6, 3sv9, 4wf8, [4wh8]], 5eqr, 5esb, 6nzt, 6p6l, 6p6m, 6p6q, 6p6r, 6p6s, 6p6t, 6p6v, 6p6z – HCVP NS3/A4 + drug
    
  • 3su0, 3su1, 3su2, 3su4, 3su5, 3su6, 3sv7, 3sv8, 4wh6, 5esq, 6c2n, 6p6o, 6vdl, 6vdm – HCVP NS3/A4 (mutant) + drug
    
• Human herpes virus 8 protease or Orf 17
  • 3njq – hOrf 17
    
  • 3njq, 5ur3, 5ute, 5utn, 5uv3, 5uvp, 5v5d, 5v5e – hOrf 17 + inhibitor
    
• Dengue virus protease
  • 3lkw – Dv12Ns2b/Dv12Ns3 (mutant) - Dengue virus 1
    
  • 4m9f, 4m9i, 4m9k, 4m9m - Dv2Ns2b/Dv2Ns3 (mutant) - Dengue virus 2
    
  • 6mo0, 6mo1, 6mo2 – Dv2Ns2b + inhibitor
    
  • 4m9t - Dv2Ns2b/Dv2Ns3 (mutant) + inhibitor
    
  • 2m9p, 2m9q – Dv2Ns2b/Dv2Ns3 + inhibitor - NMR
    
  • 3u1i – Dv3Ns2b + peptide – Dengue virus 3
    
  • 3u1j – Dv3Ns2b/Dv3Ns3 + inhibitor
    
  • 2jlq, 5yvu, 5yvv, 5yvw, 5yvy – Dv4Ns3 – Dengue virus 4
    
  • 5xc7 – Dv4Ns3 (mutant)
    
  • 5yvj – Dv4Ns2b/Dv4Ns3
    
  • 2whx – Dv4Ns2b/Dv4Ns3 + ADP
    
  • 2jlr – Dv4Ns3 + AMPPNP
    
  • 2jlu, 2jlw – Dv4Ns3 + RNA
    
  • 2jls, 2jlx, 2jly, 2jlz – Dv4Ns3 + ADP + RNA
    
  • 2jlv – Dv4Ns3 + AMPPNP + RNA
    
  • 5yw1 – Dv4Ns3 + BPTI
    
  • 2vbc, 2wzq – Dv4Ns3 residues 1475-2092 + peptide inhibitor
    
• Herpes simplex virus protease
  • 1at3 – HSV II – human herpesvirus 2
• Foot-and-Mouth Disease virus protease
  • 2bhg – FMDV residues 1650-1857 (mutant) – Foot-and-mouth disease virus
    
  • 2jqf, 2j92, 5hm2 – FMDV (mutant)
    
  • 2wv4, 2wv5 – FMDV (mutant) + peptide
    
  • 1qmy, 1qol – FMDV residues 29-201 (mutant)
    
  • 4qbb – FMDV residues 29-201 + inhibitor
    
• Infectious Bronchitis virus protease
  • 2q6d, 4x2z – IBV Ns3 – infectious bronchitis virus
    
  • 2q6f – IBV + inhibitor
• Yellowtail ascites virus protease
  • 4cx8, 4b07, 4b0t – YAV – yellowtail ascites virus
    
  • 4b08 – YAV + inhibitor
    
  • 4izj, 4izk – YAV Vp4 (mutant)
• Yellow fever virus protease
  • 6urv – NS2B + NS3
    
  • 5ffm – NS3
    
• Zika virus protease
  • 5gj4, 5gxj, 5t1v, 5tfn, 6um3, 6jpw – NS2B + NS3
    
  • 5tfo, 6um3 – NS2B + NS3 (mutant)
    
  • 5jmt, 5jps, 5jrz, 5jwh, 5txg, 5vi7, 6adw, 6mh3 – NS3
    
  • 5k8i, 5k8l, 5k8t, 5k8u, 5y4z, 5y6m, 6adx, 6ady, 6rwz, 6s0j – NS3 + nucleotide
    
  • 5gjb, 5mfx – NS3 + RNA
    
  • 5rhg, 5rhh, 5rhi, 5rhj, 5rhk, 5rhl, 5rhm, 5rho, 5rhp, 5rhq, 5rhr, 5rhs, 5rht, 5rhu, 5rhv, 5rhw, 5rhx, 5rhy– NS3 + inhibitor
    
  • 5gjc, 5gpi, 5h4i, 5h6v, 5lc0, 5yod, 5yof, 5zmq, 5zms, 5zob, 6jpw, 6kk2, 6kk3, 6kk4, 6kk5, 6kk6, 6kpq, 6l4z, 6l50, 6y3b – NS2B + NS3 + inhibitor
    
• Pseudorabies virus protease
  • 4cx8 – YAV – pseudorabies virus
    
• Coxsakievirus protease
  • 4mg3 – CSVP A2 863-1007 - Coxsakievirus A16
    
  • 3sj8 – CSVP 3C 1-183
    
  • 2vb0, 2zty, 2ztz, 3zyd – CSVP 3C 14-196 - Coxsakievirus B3
    
  • 2zu1, 3zye, 3zz3, 3zz4 – CSVP 3C (mutant)
    
  • 2ztx – CSVP 3C + Zn-H2S
    
  • 2zu3, 3zz5, 3zz6, 3zz7, 3zz8, 3zz9, 3zza, 3zzb, 3sji, 5nfs – CSVP 3C + inhibitor
    
  • 3zzc, 3zzd – CSVP 3C (mutant) + inhibitor
    
  • 3sj9 – CSVP 3C (mutant) + peptide inhibitor
    
• Human poliovirus 3C protease
  • 1l1n – HPV
    
  • 2ijd – HPV (mutant)
    
  • 4dcd – HPV + peptide inhibitor
    
• Human rhinovirus protease
  • 2in2, 2m5t – HRVP – human rhinovirus A2 - NMR
    
  • 1cqq, 2xya, 5fx5, 5fx6, 6ffn, 6ffs – HRVP + inhibitor
    
  • 6kyz, 6kz0 – HRVP + antibody – human rhinovirus B14
    
  • 2b0f – HRVP + inhibitor – NMR
    
  • 6ku7 – HRVP – human rhinovirus C
    
  • 6ku8 – HRVP + drug
    
  • 5x45 – HRVP 2A – human rhinovirus C15
    
• Human enterovirus protease A71
  • 3osy, 4ghq, 8cny – HEVP
    
  • 3r0f – HEVP (mutant)
    
  • 3sjk – HEVP (mutant) + peptide inhibitor
    
  • 4ght, 5bpe, 5c1u, 5c1x, 5c1y, 5c20, 5dp3, 5dp4, 5dp5, 5dp6, 5dp7, 5dp8, 5dp9, 5dpa, 5gso, 5gsw, 5hxf, 5wq2, 6lka, 7dnc – HEVP + inhibitor
    
  • 3sjo, 5hxf, 5wq2 – HEVP + drug
    
  • 3qzq, 3qzr, 3r0f – HEVP (mutant) + drug
    
• Human enterovirus protease B
  • 3q3x – HEVP (mutant)
    
  • 3q3y – HEVP (mutant) + inhibitor
    
  • 3ruo – HEVP + drug
    
• Human enterovirus protease D68
  • 3zv8, 8cnx – HEVP residues 1549-1731
    
  • 8fl5 – HEVP (mutant)
    
  • 3zv9, 3zva, 3zvb, 3zvc, 3zvd, 3zve, 3zvf, 3zvg, 7gnv, 7gnw, 7gnx, 7gny, 7gnz, 7go0, 7go1, 7go2, 7go3, 7go4, 7go5, 7go6, 7go7, 7go8, 7go9, 7goa, 7gob, 7goc, 7god, 7goe, 7gof, 7gog, 7goh, 7goi, 7goj, 7gok, 7gol, 7gom, 7gon, 7goo, 7gop, 7goq, 7gor, 7got, 7gou, 7gov, 7gow, 7gox, 7goy, 7goz, 7gp0, 7gp1, 7gp2, 7gp3, 7gp4, 7gp5, 7gp6, 7gp7, 7gp8, 7gp9, 7gpa, 7gpc, 7gpd, 7gpe, 7gpf, 7gpg, 7gph, 7gpi, 7gpj, 7gpl, 7gpm, 7gpn, 7gpo, 7gpp, 7gpq, 7gpr, 7gps, 7gpt, 7gpu, 7gpv, 7gpw, 7gpx, 7gpy, 7gpz, 7gq0, 7gq1, 7gq2, 7gq3, 7gq4, 7gq6, 7gq7, 7gq8, 7gq9, 7gqa, 7gqb, 7gqc, 7gqd, 7gqe, 7gqf, 7gqh, 7gqi, 7gqj, 7gqk, 7gql, 7gqm, 7gqn, 7gqo, 7gqp, 7gqq, 7gqr – HEVP + inhibitor
    
  • 7l8h – HEVP + drug
    
• Porcine epidemic diarrhea virus protease
  • 4xfq, 5hyo, 6noz – PEDVP – porcine epidemic diarrhea virus
    
  • 6l70 – PEDVP + inhibitor
    
  • 4zuh – PEDVP (mutant)+ inhibitor
    
• Echovirus 1 protease
  • 5iyt – EV1P (mutant) + inhibitor – Echovirus 1
    
• Transmissible Gastroenteritis virus protease
  • 2amp – TGEVP + inhibitor
    
• Southampton virus protease
  • 6t1q – SVP – Southampton virus
    
  • 2iph, 6t2i, 6t2x, 6t3g, 6t49, 6t4e, 6t4s, 6t5d, 6t5r, 6t6w, 6t71, 6t82, 6t8r, 6t8t, 6tal, 6taw, 6tbo, 6tbp, 6tc1, 6tcf, 6tgl – SVP + inhibitor
    
• West Nile virus protease
  • 2ggv - WNVP Ns2B/Ns3 (mutant) - West Nile virus
    
  • 2ijo - WNVP Ns2B/Ns3 (mutant) + BPTI
    
  • 2yol, 5idk, 2fp7 - WNVP Ns2B/Ns3 + peptide inhibitor
    
  • 3e90 - WNVP Ns2B/Ns3 + inhibitor
    
• African swine fever virus protease
  • 6ljb, 6lj9 – ASFV – African swine fever virus
    
• Senecavirus 3C protease residues 1509-1719
  • 6l0t – 3CP
    
• Norovirus 3C-like protease residues 1-173
  • 1wqs – 3CLP
    
• Norovirus 3C-like protease residues 1101-1281
  • 2fyq, 2fyr, 3ur6 – 3CLP
    
  • 2lnc – 3CLP - NMR
    
  • 2iph, 3ur9, 4imq – 3CLP + peptide inhibitor
    
  • 3ur9, 4imz, 4in1, 4in2, 4inh, 4xbb, 4xbc, 4xbd, 5t61, 5t62, 5t6d, 5t6f, 5t6g, 5wej, 6w5h, 6w5j, 6w5k, 6w5l – 3CLP + inhibitor
    
  • 5dg6, 5dgj, 5e0g, 5e0h, 5e0j, 5tg1, 5tg2, 6bib, 6bic, 6bid – 3CLP + macrocyclic inhibitor
    
  • 6b6i – 3CLP residues 982-1162 (mutant) - human norovirus GII
    
  • 6nir – HOV
    
• Mouse Norovirus protease residues 995-1177
  • 4ash, 4x2w, 4x2x, 4x2y, 4x2v – NS6 (mutant)
    
• SARS human corona virus 3C-like protease C-terminal 3241-3546
  • 1q2w, 1uj1, 1uk2, 1uk3, 1z1i, 2a5a, 2bx3, 2c3s, 2bx3, 2bx4, 2duc, 2gt7, 3ebn, 3vb3, 5r8t, 6m2q, 6wqf, 6xb0, 6xb1, 6xb2, 6xhu, 6y2e, 7ar5, 7ar6, 7bro, 7dqz, 7jp1, 7jpy, 7jun, 7k3t, 7kfi, 7lfp, 7khp – 3CLP – SARS-COV
    
  • 1z1j, 2gt8, 2pwx, 2q6g, 2qc2, 2qcy, 3m3s, 3m3t, 3m3v, 3fzd, 3f9e, 3f9f, 3f9g, 3f9h, 3ea7, 3ea8, 3ea9, 3eaj, 3e91, 3ee7, 3aw1, 4hi3, 5b6o, 7joy, 7n6n, 7t2v – 3CLP (mutant) – SARS-COV
    
  • 2liz – 3CLP – SARS-COV - NMR
    
  • 6wtj, 6wtk, 6wtm, 6xqs, 6xqt, 6xqu, 7aol, 7b83, 7brp, 7buy, 7c6s, 7jyc, 7k6d, 7k6e – 3CLP + drug – hCOV-2
    
  • 3d23 – 3CLP + inhibitor – hCOV-HKU1
    
  • 3tlo, 7e6l, 7e6m, 7e6n, 7e6r – NL633CLP 2940-3242 – hCOV-NL63
    
  • 5gwy, 7eov – NL633CLP + inhibitor
    
  • 1wof, 2amd, 2amq, 2amp, 2gx4, 2gz7, 2gz8, 2op9, 2ops, 2vj1, 2ynb, 2z94, 3atw, 3avz, 3d62, 3iwm, 3sn8, 3v3m, 4tww, 4twy, 4wy3, 5re4, 5re5, 5re6, 5re7, 5re8, 5re9, 5rea, 5reb, 5rec, 5red, 5ree, 5ref, 5reg, 5rep, 5rer, 5res, 5ret, 5reu, 5rew, 5rex, 5rey, 5rez, 5rf1, 5rf2, 5rf3, 5rf4, 5rf5, 5rf6, 5rf9, 5rfa, 5rfb, 5rfc, 5rfd, 5rfe, 5rff, 5rfg, 5rfh, 5rg1, 5rg2, 5rg3, 5rgg, 5rgh, 5rgi, 5rgj, 5rgk, 5rgl, 5rgm, 5rgn, 5rgo, 5rgp, 5rgq, 5rgr, 5rgs, 6lnq, 6lny, 6lo0, 6lu7, 6lze, 6m0k, 6m2n, 6w2a, 6w63, 6w79, 6wco, 6xhl, 6xhm, 6xhn, 6xho, 6xmk, 7a1u, 7aga, 7aha, 7amj, 7bqy, 7c6u, 7d1m, 7jkv, 7jpz, 7jq0, 7jq1, 7jq2, 7jq3, 7jq4, 7jq5, 7k0e, 7k0f, 7k0g, 7k0h, 7ldx, 7vic, 7xar, 8uld – 3CLP + inhibitor – SARS-COV
    
  • 5c5n, 5c5o, 8h6i – 3CLP (mutant) + inhibitor – SARS-COV
    
  • 2vj1, 3tit, 3tiu – 3CLP + unsaturated ester
    
  • 2zu2, 2zu4, 2zu5, 3aw0, 3tns, 3tnt, 3vb4, 3vb5, 3vb6, 3vb7, 7t2u – 3CLP + peptidomimetic compound
    
  • 2z9g – 3CLP + benzene + Hg
    
  • 2z9j, 2z9k, 2z9l – 3CLP + Zn compound
    
  • 1uk4, 2z3c, 2z3d, 2z3e, 2gx4, 3sna, 3snb, 3snc, 3snd, 3sne, 6xch – 3CLP + peptide inhibitor
    
  • 2gtb - 3CLP (mutant) + aza-peptide epoxide inhibitor
    
  • 2a5i, 2a5k - 3CLP + aza-peptide epoxide inhibitor
    
  • 2d2d – 3CLP + I2
    
• SARS non-human corona virus 3C-like protease C-terminal
  • 4zro – 3CLP + inhibitor – cat COV
    
  • 2yna – 3CLP + inhibitor – bat COV-HKU4
    
• SARS human corona virus papain-like protease C-terminal 1564-1878
  • 6w9c – PLpro
    
  • 7cjd, 7d6h – PLpro (mutant)
    
  • 5tl6, 5tl7, 6xa9, 6xaa, 6yva – PLpro (mutant) + mISG15
    
  • 3e9s, 3mj5, 7cjm, 7cmd – PLpro + inhibitor
    
  • 7e35, 7jrn – PLpro (mutant) + inhibitor
    
  • 6wuu, 6wx4 – PLpro + peptide inhibitor
    
  • 4mm3, 5e6j – PLpro + ubiquitin
    
  • 4m0w – PLpro (mutant) + ubiquitin
    
• MERS corona virus protease C-terminal 3248-3553
  • 5c3n, 5ko3 – ORF1A
    
  • 4wmd, 4wme, 4wmf, 8e7t – ORF1A (mutant)
    
  • 4ylu, 5wkj, 5wkk, 5wkl, 5wkm, 6vgy, 6vgz, 6vh0, 6vh1, 6vh2, 6vh3 – ORF1A + inhibitor
    
  • 4rsp, 7d3c – ORF1A + peptide inhibitor
    
  • 5zu7, 5zu9, 5zua – ORF1A + nucleotide
    
  • 5zub – ORF1A + NAD
    
  • 5hih – ORF1A macro domain 1109-1275
    
  • 5dus, 5hol – ORF1A macro domain + ADP-ribose
    
• MERS corona virus papain-like protease domain 1480-1811
  • 4rez, 4rna, 5ko3 – ORF1AB
    
  • 4r3d, 4rsp – ORF1AB + inhibitor
    
  • 4rf0, 4rf1 – ORF1AB + ubiquitin/RPL40
    
  • 5v69, 5v6a – ORF1AB + ubiquitin
    
  • 5tl6, 5tl7 – ORF1AB + ubiquitin-like protein C-terminal
    
  • 4wur – ORF1AB (mutant) + ubiquitin
    
• Mason-pfizer monkey virus protease
  • 7bgt, 7bgu – MPMVP + inhibitor
    
• Maize rayado fino virus protease
  • 7mia – MRFVP + inhibitor
    
  • 7mic – MRFVP + ubiquitin
    

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Michal Harel, Joel L. Sussman, Jaime Prilusky, Openfox