Phosphodiesterase 3D structures

3D Structures of phosphodiesterase3D Structures of phosphodiesterase

Updated on 24-August-2023

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• cAMP PDE
  • 1loi – rPDE N terminal – rat – NMR
    
  • 3ib7 – MtPDE – Mycobacterium tuberculosis
    
  • 3ib8 – MtPDE + AMP
• cGMP PDE or cyclic di-GMP PDE
  • 1ksg, 1ksh, 1ksj – hPDE δ subunit + ARF-like protein - human
    
  • 2ju4 - bPDE γ subunit – bovine - NMR
    
  • 6mzb - bPDE α,β,γ subunits – Cryo EM
    
  • 4kie, 4lyk - EcPDE EAL domain – Escherichia coli
    
  • 4lj3 - EcPDE EAL domain + GMP
    
  • 4r8z - PaPDE HD-GYP domain + Ni – Pseudomonas aeruginosa
    
  • 2bas – BsYkuI – Bacillus subtilis
    
  • 2w27 – BsYkuI + C-di-GMP
  • 3gfx, 3gfy, 3gfz, 3gg0, 3gg1 – KpBlrP1 + C-di-GMP - Klebsiella pneumoniae
    
  • 2kb2 - KpBlrP1 BLUF domain - NMR
• PDE 1
  • 4ojv – yPDE – yeast
    
  • 4ojx – yPDE + GMP
    
• PDE 1b or calcium/calmodulin-dependent 3’,5’-cyclic PDE
  • 1taz – hPDE 1b catalytic domain – human
    
  • 5up0, 5uoy - hPDE 1b catalytic domain + inhibitor
    
  • 5b25 - hPDE 1b catalytic domain (mutant) + inhibitor
    
  • 2r8q - PDE 1b catalytic domain + inhibitor – Leishmania major
    
• PDE 2A or cGMP-dependent 3’,5’-cyclic PDE
  • 1f0j – mPDE 2a regulatory domain (mutant) – mouse
    
  • 1z1l, 3ibj, 3itm - hPDE 2a catalytic domain
    
  • 3itu, 4htx, 4htz, 4jib, 4d08, 4d09, 5xkm, 5vp0, 5vp1, 5u7l, 5u7k, 5u7j, 5u7i, 5u7d, 5u00, 5tzz, 5tzx, 5tzw, 5tzh, 5tzc, 5tza, 5tz3, 6ezf, 6c7j, 6c7i, 6c7g, 6c7f, 6c7e, 6c7d, 6b98, 6b97, 6b96, 4c1i, 6cyd, 6cyc, 6cyb, 6blf, 6znd - hPDE 2a catalytic domain + inhibitor
    
  • 1f0j – mPDE 2a regulatory domain (mutant) – mouse
    
  • 6cpu - CaPDE 2 – Candida albicans
    
  • 6cpt - CaPDE 2 + IBMX
    
• PDE 2H or RNA 2’,3’-cyclic PDE
  • 5ldi - EcPDE
    
  • 5ldq - EcPDE + NADP
    
  • 5ldp, 5ldo, 5ldm, 5ldk - EcPDE + nucleotide
    
  • 5ldj - EcPDE + Pi
    
  • 5h7f, 5f7e - PDE core domain – Deinococcus radiodurans
    
• PDE 3
  • 7l27 – hPDE 3a
    
  • 7l29 – hPDE 3a + AMP
    
  • 7kwe – hPDE 3a + DNMDP
    
  • 7l28 – hPDE 3a + trequinsin
    
  • 7eg0, 7eg1, 7eg4, 7lrc, 7lrd – hPDE 3a + SLFN12 – Cryo EM
    
  • 1so2, 1soj – hPDE 3b catalytic domain + inhibitor
    
  • 5z7c – PDE 3 (mutant) – Vibrio cholerae
    
• PDE 4a
  • 3i8v, 3tvx – hPDE 4a catalytic domain + inhibitor
    
  • 6fg5, 6ezu - PDE 4a residues 230-597 – Schistosoma mansoni
    
• PDE 4b or cAMP-specific 3’,5’-cyclic PDE
  • 1f0j, 4wzi– hPDE 4b catalytic domain (mutant)
    
  • 1ro6, 1xmy, 1xn0 - hPDE 4b catalytic domain + anti-inflammatory drug
    
  • 1xot - hPDE 4b catalytic domain + drug
    
  • 1tb5, 1ro9, 1ror - hPDE 4b catalytic domain + AMP
    
  • 1y2h, 1y2j, 2qyl, 3d3p, 3kkt, 3frg, 3gwt, 3ly2, 3hmv, 3o56, 3o57, 3o0j, 3w5e, 3wd9, 4myq, 4kp6, 4nw7, 5k6j, 5ohj, 5laq, 8oeg - hPDE 4b catalytic domain + inhibitor
    
  • 4x0f - hPDE 4b catalytic domain (mutant) + inhibitor
    
  • 3g45 - hPDE 4b catalytic domain + modulator
• PDE 4c
  • 2qym – hPDE 4c catalytic domain
• PDE 4d or cAMP-specific 3’5’-cyclic PDE 4d
  • 1e9k - hPDE 4d5 N terminal – NMR
    
  • 1mkd, 1oyn, 1q9m, 1tbb, 1xoq, 3g4k, 3g4l - hPDE 4d catalytic domain + anti-inflammatory drug
    
  • 1xlx, 1xlz, 1xm4, 1xm6, 1xmu, 1xom, 1xon, 1xor, 1xos, 3iak, 6akr, 6kjz, 6kk0, 6lrm, 7cbq - hPDE 4d catalytic domain + drug
    
  • 1ptw, 1tb7 - hPDE 4d catalytic domain + AMP
    
  • 2pw3 - hPDE 4d catalytic domain (mutant) + AMP
    
  • 1y2b, 1y2c, 1y2d, 1y2e, 1y2k, 1zkn, 2fm0, 2fm5, 2qyn, 3k4s, 3sl3, 3sl4, 3sl5, 3sl6, 3sl8, 3v9b, 5wqa, 5tkb, 5k32, 5k1i, 4wcu, 4w1o, 4ogb, 6fdc, 6f8x, 6f8w, 6f8v, 6f8u, 6f8t, 6f8r, 6f6u, 5wh6, 5wh5, 5lbo, 6rcw, 6inm, 6ink, 6ind, 6imt, 6imr, 6imo, 6imd, 6imi, 6imb, 6im6, 6hwo, 6fw3, 6ftw, 6fta, 6ft0, 6fet, 6feb, 6fe7, 6fdi, 6boj, 6iag, 6ibf, 6zba, 7a8q, 7a9v, 7aag, 7ab9, 7abd, 7abe, 7abj, 7ay6, 7b9h, 7cbj, 7f2k, 7f2l, 7f2m, 7w4x, 7w4y, 7xaa, 7xab, 7xbb, 7yqf, 7ysx - hPDE 4d catalytic domain + inhibitor
    
  • 6njj, 6nji, 6njh - hPDE 4d catalytic domain (mutant) + inhibitor
    
  • 3iad, 3g4g, 3g4i, 3g58 - hPDE 4d catalytic domain + modulator
• PDE 5 or cGMP-specific 3’,5’-cyclic PDE
  • 2h40 - hPDE 5a catalytic domain
    
  • 1t9r - hPDE 5 catalytic domain
    
  • 3lfv, 3mf0, 2xss - hPDE 5a GAF domain
    
  • 1rkp, 3tgg – hPDE 5a1 catalytic domain (mutant) + inhibitor
    
  • 2chm, 4oex, 4oew, 4g2w, 4g2y, 4i9z, 4ia0, 4md6, 5jo3, 6acb, 5zz2, 6iwi, 6vbi, 7far - hPDE 5a catalytic domain + inhibitor
    
  • 2h44, 3bjc, 3hc8, 3hdz, 3shy, 3shz, 3sie, 3tge - hPDE 5a1 catalytic domain + inhibitor
    
  • 1udt, 1udu, 1uho, 1tbf, 1xoz, 1xp0, 2h42, 3b2r, 6l6e - hPDE 5 catalytic domain + drug
    
  • 3jwq - hPDE 5/hPDE 6 catalytic domain + drug
    
  • 3jwr - hPDE 5/hPDE 6 catalytic domain + hPDE γ subunit peptide + inhibitor
    
  • 1t9s - hPDE 5 catalytic domain + GMP
    
  • 2k31 - mPDE 5a cGMP-binding domain – NMR
    
  • 5w10 - PDE + cAMP – Leptospira interrogans
    
• PDE 6 or retinal rod rhodopsin-sensitive cGMP 3’,5’-cyclic PDE
  • 5t4x, 7pac - hPDE 6d δ subunit
    
  • 3t5g – hPDE 6d δ subunit + GTP-binding protein RHEB
    
  • 3t5i - hPDE 6d δ subunit + GTP-binding protein RHEB peptide
    
  • 5tar, 5tb5, 7q9u - hPDE 6d δ subunit + GTP-binding protein KRas
    
  • 7qf9 - hPDE 6d δ subunit + KRas peptide
    
  • 5f2u - hPDE 6d δ subunit + INPP5E peptide
    
  • 5e8f - hPDE 6d δ subunit + PDE 6c peptide
    
  • 4jhp - hPDE 6d δ subunit + RPGR
    
  • 4jv6, 4jv8, 4jvb, 4jvf, 5ml2, 5ml3, 5ml4, 5ml6, 5ml8, 5nal, 5e80, 7pad, 7pae, 7qjk, 7faq - hPDE 6d δ subunit + inhibitor
    
  • 6mzb, 7jsn - bPDE 6 g subunit in visual signaling complex – Cryo EM
    
  • 3dba - cPDE 6c GAF A domain – chicken
    
  • 6x88 - cPDE 6c a subunit GAF domain 1-862
    
• PDE 7
  • 1zkl, 3g3n, 2y2b, 4y2b, 4pm0 – hPDE 7a catalytic domain + inhibitor
    
• PDE 8
  • 3ecm – hPDE 8a catalytic domain
    
  • 3ecn, 7cwf, 7cwg, 7vsl, 7vtv, 7vtw, 7vtx – hPDE 8a catalytic domain + inhibitor
    
  • 7cwa - hPDE 8a catalytic domain + leukemia drug
    
• PDE 9
  • 2hd1, 2yy2, 3jsi, 3jsw, 3k3e, 3k3h, 4e90, 4g2j, 4g2l, 4gh6,4y8c, 4y87, 4y86, 6a3n, 6lzz, [[[7f0i]], [8bpy]] - hPDE 6d δ subunit + RPGR
    
  • 3n3z, 3qi3, 3qi4 - hPDE 9a catalytic domain (mutant) + inhibitor
    
  • 3dy8, 3dyl, 3dyn, 3dyq, 3dys - hPDE 9 catalytic domain + GMP
    
  • 4qge - PDE 9 catalytic domain + inhibitor - chimpanzee
    
  • 4gyz - mPDE 9 catalytic domain + AMP
    
• PDE 10 or cAMP and cAMP-inhibited cGMP 3’,5’-cyclic PDE
  • 2oup - hPDE 10a catalytic domain
    
  • 2zmf – hPDE 10a C terminal
    
  • 2ous, 2ouv - hPDE 10a2 catalytic domain (mutant)
    
  • 2qyk, 3lxg, 2y0j, 3qpn, 3qpo, 3qpp, 3sn7, 3sni, 3snl, 3wi2, 4ael, 4ajd, 4ajf, 4ajg, 4ajm, 4ddl, 4fcb, 4fcd, 4heu, 4hf4, 4lkq, 4llj, 4llk, 4llp, 4llx, 4lm0, 4lm1, 4lm2, 4lm3, 4lm4, 4muw, 4mvh, 4yqh, 4ys7, 3ws8, 3ws9, 3wyk, 3wyl, 3wym, 4mrw, 4mrz, 4ms0, 4msa, 4msc, 4mse, 4msh, 4msn, 5uwf, 5k9r, 5i2r, 5edi, 5edh, 5edg, 5ede, 5dh5, 5dh4, 5c2h, 5c2e, 5c2a, 5c29, 5c28, 5c1w, 5b4k, 5b4l, 5axq, 5axp, 4zo5, 4xy2, 4wn1, 4tpp, 4tpm, 4phw, 4p1r, 4p0n, 5xuj, 5xui, 6msc, 6msa, 6ke0, 6kdz, 6kdx, 6iji, 6ijh, 5znl, 6ko0, 6ko1, 6kze, 7bpi, 7qpm - hPDE 10a catalytic domain + inhibitor
    
  • 2wey, 3hqw, 3hqy, 3hqz, 3hr1, 3ui7, 3uuo, 4bbx, 4dff, 8di4 - hPDE 10a catalytic domain + schizophrenia drug
    
  • 2oun - hPDE 10a2 catalytic domain + AMP
    
  • 2our, 2ouy - hPDE 10a2 catalytic domain (mutant) + AMP
    
  • 2ouq - hPDE 10a2 catalytic domain + GMP
    
  • 2ouu - hPDE 10a2 catalytic domain (mutant) + GMP
    
  • 2o8h – rPDE 10a catalytic domain
    
  • 6k9u, 2ovv, 2ovy - rPDE 10a catalytic domain + inhibitor
    
• PDE 12
  • 4zkf, 4z0v - hPDE
    
  • 4z2b - hPDE + inhibitor
    
• PDE b1
  • 4i15 – TbPDEb1 catalytic domain – Trypanosoma brucei
    
  • 5l9h, 5l8y, 5l8c, 5g5v, 5g57, 5g2b, 4phl, 6rgk, 6rfw, 6rfn, 6rb6, 6gxq, 6fv9, 6ftm, 6frd, 6fe3, 6fdx, 6fdw, 6fds, 6qgp, 6qgu, 7a28, 7a2f – TbPDEb1 catalytic domain + inhibitor
    
• PDE b2
  • 5h2r, 5h2q – TbPDEb2 catalytic domain + inhibitor
    
• U6 snRNA PDE
  • 5v1m - hPDE + UMP
    
  • 6d31 - hPDE + AMP
    
  • 6d30, 6d2z - hPDE (mutant) + RNA
    
  • 5uqj - yPDE
    
• Diguanylate PDE
  • 5mkg, 5mf5 - PaPDE + c-di-GMP
    
  • 5mfu - PaPDE + GMP + Mn
    
  • 5m1t - PaPDE + c-di-GMP + Mg
    
• Sphingomyelin PDE see Sphingomyelinase
• 1-phosphatidylinositol PDE see Phospholipase C
• C-di-GMP PDE See C-di-GMP specific phosphodiesterases
• Cyclic nucleotide PDE
  • 1woj – hPDE residues 166-379
    
  • 2ilx - rPDE catalytic domain
    
  • 2xmi, 2y1p, 2y3x, 5ae0 - mPDE catalytic domain
    
  • 4wex, 4wdh, 4wde, 4wdd, 4wcc, 4wcb, 4wca, 4wc9, 4wbl, 4wbi, 7qzk, 7qzs - mPDE catalytic domain (mutant)
    
  • 1mc0 – mPDE regulatory subunit
    
  • 2ydb - mPDE catalytic domain + cyclic NADP
    
  • 3zbr, 3zbs, 3zbz - mPDE catalytic domain (mutant) + NADP
    
  • 2ydc - mPDE catalytic domain + GTP
    
  • 2ydd - mPDE catalytic domain + cyclic AMP
    
  • 2ypc, 2ype, 2yph - mPDE catalytic domain (mutant) + cyclic AMP
    
  • 2yoz, 2yp0, 4wfr - mPDE catalytic domain + 2’-AMP
    
  • 2yq9, 4wdb, 4wda - mPDE catalytic domain (mutant) + 2’-AMP
    
  • 4wdg, 4wdf - mPDE catalytic domain (mutant) + 2’-ADP
    
  • 1fsi, 1jh6 – AtPDE – Arabidopsis thaliana
    
  • 1jh7 – AtPDE + inhibitor
    
  • 3jyf – KpPDE residues 16-354
    
  • 3v93 – TcPDE catalytic domain – Trypanosoma cruzi
    
  • 3v94 - TcPDE catalytic domain + inhibitor
    
• Tyrosyl-DNA PDE
  • 1jy1, 1qzq – hPDE1 catalytic domain
    
  • 1mu7 - hPDE1 catalytic domain (mutant) + WO4
    
  • 1mu9 - hPDE1 catalytic domain (mutant) + VO4
    
  • 1nop, 1rff, 1rfi, 1rg1, 1rg2, 1rgt - hPDE1 catalytic domain (mutant) + DNA + topoisomerase peptide + VO4
    
  • 1rgu, 1rh0 - hPDE1 catalytic domain (mutant) + polynucleotide + neurohormone
    
  • 6n19, 6n17, 6n0r, 6n0o, 6n0n, 6n0d, 6mz0, 6myz, 6mj5, 6djj, 6dji, 6djh, 6djg, 6djf, 6dje, 6djd, 6dim, 6dih, 6die, 6dhu, 6w4r, 6w7j, 6w7k, 6w7l, 7ufy, 7ufz, 8cvq, 8cw2 - hPDE catalytic domain + inhibitor
    
  • 5j3s, 5j3p - hPDE catalytic domain (mutant) + inhibitor
    
  • 5nwa, 5nw9 – hPDE1 residues 1-148 + DNA
    
  • 6q00, 6q01 - hPDE UBA domain 25-66 + ubiquitin
    
  • 5j3s, 5j3p - hPDE1 catalytic domain (mutant) + inhibitor
    
  • 5inm - mPDE catalytic domain
    
  • 5inn - mPDE catalytic domain (mutant)
    
  • 4gz0, 4gz1, 4gz2, 4puq, 5inq, 5inp, 5ino, 5inl, 5ink, 5ht2 – mPDE catalytic domain + DNA
    
  • 5tvq – mPDE catalytic domain + SUMO-2
    
  • 5tvp – mPDE catalytic domain + SUMO-2 + DNA
    
  • 5j42, 5j3z - mPDE catalytic domain (mutant) + inhibitor
    
  • 4f1h, 4fpv – zPDE + DNA – zebra fish
    
  • 6ca4 - zPDE catalytic domain (mutant) + inhibitor
    
  • 4f1i, 4fva, 4gew – PDE – Caenorhabditis elegans
    
  • 1q32 – yPDE
    
  • 3sq3, 3sq5, 3sq7, 3sq8 – yPDE (mutant)
    
• Glycerophosphodiester PDE
  • 1o1z – TmPDE – Thermotoga maritima
    
  • 1t8q, 1ydy – EcPDE
    
  • 1v8e – TtPDE – Thermus thermophilus
    
  • 1vd6 – TtPDE + glycerol
    
  • 1zcc – PDE – Agrobacterium tumefaciens
    
  • 2o55 – PDE – Galdieria sulphuraria
    
  • 2oog, 2p76 – SaPDE – Staphylococcus aureus
    
  • 2otd – PDE – Shigella flexneri
    
  • 3ch0 – PDE – Cytophaga hutchisonii
    
  • 2pz0 – PDE – Thermoanaerobacter tengcongensis
    
  • 2zo9, 2zoa – PDE + malonate – Enterobacter aerogenes
    
  • 3mz2, 3no3 – PDE – Parabacterioides distasonia
    
  • 4oec – PDE – Thermococcus kodakarensis
    
  • 5t9c, 5t9b – BsPDE + P3G
    
  • 5t91 – BsPDE + bicine
    
  • 7e0v – PfPDE – Pyrococcus furiosus
    
  • 7e2a – PfPDE (mutant)
    
  • 7e2b – PfPDE + palmitate + choline
    
• PDE
  • 5gz4 – TacPDE – Taiwan cobra
    
  • 5gz5 – TacPDE + AMP
    
  • 7cba – TacPDE + flavonoid
    
  • 2ahd – PDE – Methanocaldococcus jannaschii
    
  • 3qvq – PDE + P3G– Oleispira antarctica
    
  • 4b2o – BsPDE
    
  • 4g75, 4g76 – PaPDE
    
  • 5xsi – SaPDE catalytic domain
    
  • 5xt3 – SaPDE catalytic domain + C-di-GMP
    
  • 5xsn – SaPDE catalytic domain + C-di-AMP
    
  • 5xsp – SaPDE catalytic domain + AMP
    
  • 5vyd, 7d7p – SrPDE PDE domain 387-704 – Salpingoeca rosetta
    
  • 7cj3, 7d7q – SrPDE TM domain 33-378
    
  • 5o7f – TmPDE (mutant) + GMP
    
  • 5o1u – TmPDE + AMP
    
  • 5o70, 5o4z – TmPDE (mutant) + AMP
    
  • 5o58 – TmPDE (mutant) + RNA
    
  • 7dck – PDE tw9814 + RNA – Epsilonproteobacteria bacterium