Proteinase 3D structures
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3D structures of proteinase
Updated on 13-August-2026
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- Proteinase A or saccharopepsin
- 1fmu, 1fmx, 2jxr – yPRO - yeast
- 1dp5, 1dpj, 1g0v - yPRO + polypeptide inhibitor IA3
- 1fq5, 1fq6, 1fq7, 1fq8 - yPRO + inhibitor
- 2sga – SgPRO – Streptomyces griseus
- 1sgc - SgPRO + chymostatin A
- 3sga, 4sga, 5sga - SgPRO + polypeptide inhibitor
- 4fvd – hevPRO 2A + peptide – human enterovirus
- 4fvb – hevPRO 2A (mutant)
- 31mr – SpPRO + antibody – Streptococcus pyogenes – Cryo EM
- 1fmu, 1fmx, 2jxr – yPRO - yeast
- Proteinase B
- Proteinase K
- 1cnm, 1egq, 2g4v, 2id8, 2prk, 2v8b, 3aj8, 3aj9, 3d9q, 3ddz, 3de0, 3de1, 3de2, 3de3, 3de4, 3de5, 3de6, 3de7, 3dvq, 3dvr, 3dvs, 3dw1, 3dw3, 3dwe, 3gt3, 3gt4, 3i2y, 3i30, 3i34, 3i37, 3l1k, 3q40, 3q5g, 3qmp, 4b5l, 4fon, 5amx, 5avj, 5avk, 5b1d, 5b1e, 5kxu, 5kxv, 5mjl, 5uvl, 5whw, 5wjg, 5wjh, 6cl7, 6cl8, 6cl9, 6cla, 6clb, 6fjs, 6j43, 6k2p, 6k2r, 6k2s, 6k2t, 6k2v, 6k2w, 6mn6, 6n4u, 6pu4, 6pu5, 6pq0, 6pq4, 6qf1, 6rzp, 6v8r, 7c0p, 7nuz, 7s4z, 8f05, 8f06, 8f07, 8rse, 8rsf, 8rsg, 8sog, 8sqv, 9fu1, 9ftx, 9fty, 9kw1 – EaPRO + Ca – Engyodontium album
- 5cw1, 5roc, 5rod, 5roe, 5rog, 5roh, 5roi, 5roj, 5rok, 5rom, 5roo, 5ros, 5rot, 5rou, 5rov, 5rox, 5roy, 5roz, 5rp0, 5rp1, 5rp2, 5rp3, 5rp4, 5rp5, 5rp8, 5rpb, 5rpe, 5rpf, 5rpi, 5rpn, 5rpo, 5rpp, 5rpq, 5rpr, 5rps, 5rpt, 5rpu, 5rpv, 5rpw, 5rpx, 5rpy, 5rpz – EaPRO
- 7ln7, 7lpt, 7lpu, 7lpv, 7lq8, 7lq9, 7lqa, 7lqb, 7lqc, 7ltd, 7lti, 7ltv, 7lu0, 7lu1, 7lu2, 7lu3 - EaPRO + Ca – radiation damage
- 1ic6, 6qxv – EaPRO (mutant) + Ca
- 1ht3, 1ptk – EaPRO + Ca + Hg
- 2pkc, 7a68 – EaPRO + Na
- 5wrc, 6k2x – EaPRO + Pr
- 6txg – EaPRO + Ru
- 5rof, 5rol, 5ron, 5ror, 5row, 5rp6, 5rp7, 5rp9, 5rpa, 5rpc, 5rpd, 5rpg, 5rph, 5rpk, 5rpl, 5rpm – EaPRO + fragment
- 4dj5, 4wob, 4woc, 7njj, 7nuy – EaPRO
- 6clb, 6cla, 6cl9, 6cl8, 6cl7, 6pkt, 6pks, 6pkr, 6pkq, 6pkp, 6pko, 6pkn, 6pkm, 6pkl, 6pkk, 6pkj, 6law, 6zet, 6zeu, 6zev, 7skx, 7svy, 7svz, 7sw0, 7sw1, 7sw2, 7sw3, 7sw4, 7sw5, 7sw6, 7sw7, 7sw8, 7sw9, 7swa, 7swb, 7swc, 8e52, 8e53, 8fyo, 8fyp, 8fyq, 8fyr, 8fys, 8sdk – EaPRO - MicroED
- 5i9s, 5k7s, 9dho, 9n0f, 9n0g, 9n0h, 9odv, 9odw, 9oyy, 9ozu – EaPRO + Ca – MicroED
- 1cnm, 1egq, 2g4v, 2id8, 2prk, 2v8b, 3aj8, 3aj9, 3d9q, 3ddz, 3de0, 3de1, 3de2, 3de3, 3de4, 3de5, 3de6, 3de7, 3dvq, 3dvr, 3dvs, 3dw1, 3dw3, 3dwe, 3gt3, 3gt4, 3i2y, 3i30, 3i34, 3i37, 3l1k, 3q40, 3q5g, 3qmp, 4b5l, 4fon, 5amx, 5avj, 5avk, 5b1d, 5b1e, 5kxu, 5kxv, 5mjl, 5uvl, 5whw, 5wjg, 5wjh, 6cl7, 6cl8, 6cl9, 6cla, 6clb, 6fjs, 6j43, 6k2p, 6k2r, 6k2s, 6k2t, 6k2v, 6k2w, 6mn6, 6n4u, 6pu4, 6pu5, 6pq0, 6pq4, 6qf1, 6rzp, 6v8r, 7c0p, 7nuz, 7s4z, 8f05, 8f06, 8f07, 8rse, 8rsf, 8rsg, 8sog, 8sqv, 9fu1, 9ftx, 9fty, 9kw1 – EaPRO + Ca – Engyodontium album
- Proteinase K complex with peptide
- 1p7v, 1p7w, 3prk – EaPRO + Ca + peptide inhibitor
- 1bjr, 2dqk, 2duj – EaPRO + Ca + lactoferrin peptide
- 2hd4 – EaPRO + Ca + lactoferrin peptide inhibitor
- 2dp4, 3ptl – EaPRO + lactoferrin peptide
- 1pek, 1pfg, 4zar – EaPRO + peptide inhibitor
- 1pj8 – EaPRO + Hg + substrate analog peptide
- 2hpz, 2pq2, 6kkf 8sou, 8sov, 8spl – EaPRO + Ca + peptide
- 3osz – EaPRO + Ca + antimicrobial peptide
- 2b6n – PRO + tripeptide - Serratia
- 1p7v, 1p7w, 3prk – EaPRO + Ca + peptide inhibitor
- Proteinase K complex with small molecule
- 2pwb – EaPRO + Ca + coumarin
- 2pyz – EaPRO + Ca + auramine
- 2pwa – EaPRO + Ca + alanine boronic acid
- 1oyo – EaPRO + Ca + melanin monomer
- 3dyb – EaPRO + Ca + digalacturonic acid
- 6rve, 6rvg, 6rug, 6ruh, 6ruk, 6run, 6ruw, 7a9f, 7a9k, 7a9m – EaPRO + keggin derivative
- 6k8m – EaPRO + urea derivative
- 7jsy – EaPRO + triiodoisophthalate derivative - MicroED
- 2pwb – EaPRO + Ca + coumarin
- Proteinase 3C
- 1hav, 1qa7 – hvPRO – Hepatitis virus
- 2h6m, 2h9h, 2hal – hvPRO + peptide inhibitor
- 2vb0, 2zu3, 2zty, 2ztz, 3zyd - PRO – Coxsakievirus
- 2zu1, 3zye – csvPRO (mutant)
- 2ztx – csvPRO + inhibitor
- 3zz3, 3zz4, 3zz5, 3zz7, 3zz8, 3zz9, 3zza, 3zzb, 3zzc, 3zzd – csvPRO (mutant) + inhibitor
- 4ghq – hevPRO
- 4ght – hevPRO + common cold drug
- 4ghq – evPRO - Enterovirus
- 4ght, 5c1u, 5c1x, 5c1y, 5c20, 5dp3 5dp4, 5dp5, 5dp6, 5dp7, 5dp8, 5dp9, 5dpa, 6lka, 7dnc – evPRO + inhibitor
- 5hm2 – PRO - Foot-and-mouth virus
- 1l1n – PRO - polio virus
- 1hav, 1qa7 – hvPRO – Hepatitis virus
- PRO 3C-like see Virus protease
- Thermostable neutral proteinase see Thermolysin
- Calcium-activated neutral PRO see Calpain
- Papaya PRO I see Papain
- Thermostable neutral PRO see Thermolysin
- H2-Proteinase
- 1wni – PRO – Trimeresurus flavoviridis
- Aspartic Proteinase
- 1fq4 - yPRO + inhibitor
- 2asi – RmPRO – Rhizomucor miehei
- 2rmp – RmPRO + pepstatin
- 1zap – CaPRO – Candida albicans
- 1eag – CaPRO 2 + inhibitor
- 2h6s – CaPRO 3
- 2h6t – CaPRO 3 + pepstatin
- 2qzx – CaPRO 5 + pepstatin
- 4ybf – CpPRO – Candida parapsilosis
- 4y9w – CpPRO + peptide
- 1izd - AoPRO – Aspergillus oryzae
- 1ize - AoPRO + polypeptide-statin inhibitor
- 1j71 - PRO + polypeptide inhibitor – Candida tropicalis
- 1wkr - PRO + polypeptide-statin inhibitor – Irpex lacteus
- 3apr - PRO + polypeptide inhibitor – Rhizopus chinesis
- 1epl, 1epm, 2er0, 2er9, 4er4 - fuPRO + polypeptide inhibitor – fungus
- 1epo, 1epp, 1epq - fuPRO + intermediate
- 3emy - PRO + pepstatin – Hypocrea jecorina<br />
- 1mpp - PRO – Mucor pusillus
- 3c9x - PRO – Trichoderma reesei
- 1epr - PRO – chestnut blight fungus
- 2apr - PRO – Rhizopus microsporus
- 1fq4 - yPRO + inhibitor
- Aspartic PRO from Plasmodium vivax see Plasmepsin
- Aspartic PRO from Penicillium janthinelium see Penicillopepsin
- Cysteine Proteinase or gingipain
- 1a6r, 2dzy, 2dzz, 2e00, 2e01, 2e02, 2e03 – yPRO 1 (mutant)
- 2hrv – PRO 2A – human rhinovirus
- 3m1h, 4itc – PgPRO adhesion domain residues 982-1154 – Porphyromonas gingivalis
- 1cvr, 4rbm, 4tkx – PgPRO catalytic domain residues 229-683
- 6i9a – PgPRO catalytic domain + inhibitor
- 5mun – PgPRO residues 20-228
- 7pq4 – PgPRO C-terminal residues 662-736 - NMR
- 2fo5 – PRO residues 133-356 + leupeptin – Hordenum vulgare
- 1cv8, 1x9y – SaPRO – Staphylococcus aureus
- 1pxv, 1y4h – SaPRO + PRO inhibitor
- 6p4e – PRO B (mutant) – Leishmania mexicana
- 1z8r – csvPRO
- 2fyq, 2fyr – PRO residues 1101-1281 – Norwalk virus
- 2jtc, 2uzj – SpPRO
- 6ukd, 6uqd – SpPRO + inhibitor
- 1a6r, 2dzy, 2dzz, 2e00, 2e01, 2e02, 2e03 – yPRO 1 (mutant)
- For Trypanosoma cruzi cysteine proteinase see Cruzain
- Serine Proteinase
- 5m3n – hPRO HTRA2 134-458 – human
- 1lcy, 5fht, 5m3o, 5tny, 5tnz, 5to0, 5to1, 5wyn, 7vge – hPRO HTRA2 134-458 (mutant)
- 2pzd – hPRO HTRA2 PDZ domain 359-458
- 8auk – hPRO HTRA2 134-458 + BIRC6 – Cryo EM
- 8e2k – hPRO HTRA2 (mutant) + BIRC6 – Cryo EM
- 1toc – PRO – bovine
- 3s9a, 3s9b – RvPRO – Siamese Russell’s viper
- 3s9c, 3sbk – RvPRO + human factor V polypeptide
- 1op0, 1op2 – PRO – Chinese moccasin
- 1qy8, 1wcz – SaPRO
- 1mbm – PRO – equine arteritis virus
- 1dbi – PRO – Bacillus
> - 1ga1, 1ga4, 1ga6, 1nlu – PsPRO + iodotyrostatin fragment – Pseudomonas
- 6m8c, 6m8d, 6m8f, 6m9y, 6m9w - PsPRO + polypeptide inhibitor
- 1s2n, 1sh7 – PRO – Vibrio
- 8c4z – PRO (mutant) – Thermus
- 2sfa – PRO – Streptomyces fradiae
- 5m3n – hPRO HTRA2 134-458 – human
- For enamel matrix serine proteinase 1 see Kallikrein
- For cytotoxic T-lymphocyte proteinase 1 see Granzyme
- Proteinase yscE or yeast 20S proteasome or yeast 13S proteasome
- 8rvq, 9d35, 9d3i, 9d4c, 9d4u, 9rl3, 9rla, 9rlt, 9rlz, 9rm0, 9rm1 – yPRO yscE – Cryo EM
- 7ls5, 7ls6, 7lsx, 7tej, 8rvl, 8rvo, 8rvp, 8t08, 8t0m, 8u6y, 8u7u – yPRO yscE (mutant) – Cryo EM
- 4g4s, 4r18, 5cz4, 5l5a, 5l5b, 5l5w, 6htb, 6hv3, 9aw5, 9aw6, 9frw – yPRO yscE
- 3wxr, 4qux, 4quy, 4qv0, 4qv1, 4qv3, 4qv4, 4qv5, 4qv6, 4qv7, 4qv8, 4qv9, 4y8m, 4y8r, 4y9y, 4ya1, 4ya4, 5bxl, 5cgf, 5cza, 5d0w, 5fg9, 5fga, 6hwc, 9qaf, 9qbi, 9qc9, 9qcf, 9qck – yPRO yscE (mutant)
- 9s78 – yPRO yscE + drug – Cryo EM
- 2f16, 3d29, 3mg0, 4q1s, 4qvl, 5l5e, 5l5f, 5l5y, 5l5z, 5l65, 5l66, 9qb1, 9qb4 – yPRO yscE + drug
- 2gpl, 4qvm, 4qvn, 4qvq, 4qvv, 4qvw, 4qvy, 4qw7, 4qwf, 4qwg, 4qwi, 4qwj, 4qwk, 4qwl, 5bxn, 5cz5, 5cz7, 5cz8, 5cz9, 5d0s, 5d0v, 5d0x, 5d0z, 5fgd, 5fge, 5fgf, 5fgg, 5fgi, 5fhs, 6hwd, 6hwe, 9qbw, 9qdf, 9qds – yPRO yscE (mutant) + drug
- 10mt, 10og, 10qt, 10sj – yPRO yscE + DNA – Cryo EM
- 7teo – yPRO yscE + FUB1 – Cryo EM
- 3un4 – yPRO yscE + morpholine
- 1g65, 1jd2, 2fak, 2zcy, 3bdm, 3dy3, 3dy4, 3e47, 3gpj, 3gpt, 3gpw, 4gk7, 3hye, 3mg4, 3mg6, 3mg7, 3mg8, 3nzj, 3nzw, 3nzx, 3oeu, 3oev, 3okj, 3sdi, 3sdk, 3shj, 3tdd, 3un8, 4eu2, 4fzc, 4fzg, 4hnp, 4hrc, 4hrd, 4inr, 4int, 4inu, 4jsq, 4jsu, 4jt0, 4lqi, 4ltc, 4nnn, 4qwx, 4r17, 4rur, 4x6z, 4y69, 4y6a, 4y6v, 4y6z, 4y70, 4y74, 4y75, 4y77, 4y78, 4y7w, 4y7x, 4y7y, 4y80, 4y81, 4y82, 4y84, 4y8g, 4y8h, 4y8i, 4y8j, 4y8k, 4y8l, 4y8n, 4y8o, 4z1l, 5ahj, 5bou, 5dki, 5dkj, 5fg7, 5l52, 5l54, 5l55, 5l5d, 5l5h, 5l5i, 5l5j, 5l5o, 5l5p, 5l5q, 5l5r, 5l5s, 5l5t, 5l5u, 5l5v, 5l5x, 5l60, 5l61, 5l62, 5l63, 5l64, 5l67, 5l68, 5l69, 5l6a, 5l6a, 5l6c, 5lai, 5laj, 5ltt, 5m2b, 6g7f, 6g8m, 6g8n, 6gop, 6htc, 6htd, 6htr, 6hv4, 6hv5, 6hv7, 6hva, 6hvr, 6hvs, 6hvt, 6hvu, 6hvv, 6hvw, 6hvx, 6hvy, 6hw0, 6hw3, 6hw4, 6hw5, 6hw6, 6hw7, 6hw8, 6hw9, 6hwa, 6hwb, 6zou, 6zp6, 6zp8, 7o2l, 8ohz, 8oi1, 8olr, 8rhj, 8rhk, 8rhl, 9aw7, 9c97, 9ey9, 9fst, 9fsv, 9fsu, 9ft0, 9ft1, 9qai – yPRO yscE + inhibitor
- 4y8p, 4y8q, 4y8s, 4y8t, 4y8u, 4y9z, 4ya0, 4ya2, 4ya3, 4ya5, 4ya7, 4ya9, 5cgg, 5cgh, 5cgi, 5cz6, 5d0t, 5fgh, 6htb, 6htc, 6htd,6htp, 6htr, 6hub, 6huc, 6huq, 6huu, 6huv, 6hwf, 9aw3, 9qbe, 9qbo, 9qby, 9qd2 – yPRO yscE (mutant) + inhibitor
- 4nnw, 4no1, 4no6, 4no8, 4no9, 4qby, 4qlq, 4qls, 4qlt, 4qlu, 4qlv, 5jhr, 5jhs, 6h39, 8bw1 – yPRO yscE + peptide inhibitor
- 1z7q, 4v7o, 5nif – yPRO yscE + activator
- 9d0t, 9gbk – yPRO yscE + regulator – Cryo EM
- 8rvq, 9d35, 9d3i, 9d4c, 9d4u, 9rl3, 9rla, 9rlt, 9rlz, 9rm0, 9rm1 – yPRO yscE – Cryo EM
- Astacin
