Immunodeficiency virus protease

From Proteopedia

Revision as of 10:15, 16 July 2017

3D structures of immunodeficiency protease

Updated on 16-July-2017 {{#tree:id=OrganizedByTopic|openlevels=0|

• HIV-I protease

• • 4yob, 4npu, 3u71, 2g69, 1lv1, 1odx – HIVP (mutant) – HIV-I virus
    
  • 2hvp, 1odw, 3phv – HIVP
    
  • 5uov, 5upz, 5ult, 5bry, 5bs4, 4mc1, 4mc2, 4mc6, 4mc9, 2q3k, 3th9 5ult – HIVP (mutant) + sulfonamide inhibitor
    
  • 3qrm, 3qpj, 3qbf, 3ckt, 3qro, 3qrs, 4gb2 – HIVP (mutant) + pyrrolidine inhibitor
    
  • 1hte, 1htf, 1htg – HIVP + penicillin inhibitor
    
  • 5kqx, 5kqy, 5kqz, 5kr0, 5kr1, 5kr2, 5b18, 4ll3, 4jec, 3tkg, 3tkw, 3tl9 – HIVP + drug
    
  • 5t8h, 5e5j, 5e5k, 4yoa, 4q5m, 3swj, 4npt, 4qgi, 3s43, 3s45, 3s53, 3s54, 3s56, 3d1x, 3cyw, 3cyx, 3d1z, 3d20, 3bvb, 2r5p, 2r5q, 2hs1, 2hs2, 2q5k, 2nmy, 2nmz, 2nnk, 2nnp, 2fxe, 2o4l, 2o4s, 2fgu, 2fgv, 3so9, 3spk, 3k4v, 1fb7, 2fxd, 2fxe, 3el4, 3el5, 3el9, 2z54 – HIVP (mutant) + drug
    
  • 4u7q, 4u7v, 4u8w, 4i8z, 4i8w, 3t11, 4fe6, 4a6b, 4a6c, 4dfg, 4dqb, 3gga, 3ggx, 2pwc, 2pwr, 2qnn, 2fde, 3kfr, 3kfs, 3tlh, 1hiv, 1hps, 1hpv, 1hvi, 1hvj, 1hvk, 1hvl, 1sbg, 1sh9, 1upj, 1w5v, 2uxz, 2uy0, 2zga, 3dcr, 3s85, 3zps, 3zpt, 3zpu, 4phv, 9hvp, 1c6x, 1c6y, 1c6z, 1c70, 1hxb, 2a4f, 1hos, 5ivq, 5ivr, 5ivs, 5ivt, 2upj – HIVP + inhibitor
    
  • 5jfp, 5jfu, 5jg1, 5kao, 5dgu, 5dgw, 5agz, 5ah6, 5ah8, 5ah9, 5aha, 5ahb, 5ahc, 5ah7, 4cpq, 4cpr, 4cps, 4cpt, 4cpu, 4cpw, 4cpx, 4coe, 4cp7, 4m8x, 4m8y, 3vf5, 3vf7, 3vfa, 3vfb, 4a4q, 3tof, 3tog, 3toh, 4djo, 4djp, 4djq, 4djr, 3sa3, 3sa4, 3sa5, 3sa6, 3sa7, 3sa8, 3sa9, 3saa, 3sab, 3sac, 4dqc, 4dqe, 4dqf, 4dqg, 4dqh, 3qrm, 3qro, 3qrs, 3qp0, 3qpj, 3qn8, 3qih, 3qbf, 3qaa, 3h5b, 3dk1, 3djk, 2r43, 3d1y, 2qci, 2qd6, 2qd7, 2qd8, 2qhy, 2qhz, 2qi1, 2qi7, 2z4o, 3bva, 3bxr, 3bxs, 2q54, 2j9j, 2j9k, 2je4, 2hc0, 2psu, 2psv, 2i0a, 2i0d, 2f3k, 2idw, 2ien, 2ieo, 2hb3, 1zbg, 2f80, 2f81, 2f8g, 2azc, 2a1e, 2fdd, 2aoc, 2aod, 2aoe, 1w5w, 1w5x, 1w5y, 3i7e, 1bdq, 1bwa, 1bwb, 1gnm, 1gnn, 1mrx, 1msn, 1sgu, 1t7i, 2pk5, 2pk6, 2r38, 2r3t, 3fx5, 3h5b, [[3i6o, 3kdb, 3kdc, 3kdd, 3ok9, 3qaa, 3st5, 4hdb, 4hdf, 4hdp, 4he9, 4heg, 4kb9, 4zip, 5cok, 5con, 5coo, 5cop, 2xye, 2xyf, 4zls, 1axa, 1hef, 1heg, 1a8k, 1aaq – HIVP (mutant) + inhibitor
    
  • 2zye – HIVP (mutant) + inhibitor - neutron
    

• HIV-I protease complex with peptide

• • 4tvg, 5hvp – HIVP + pepstatin peptide
    
  • 4f73, 4f74, 4f75, 4f76, 4ep2, 4ep3, 4epj, 4eq0, 4eqj – HIVP + substrate peptide
    
  • 4fae, 4faf, 2fns, 2fnt, 1f7a, 1kj4, 1kj7, 1kjf, 1kjg, 1kjh, 1tsq, 1tsu, 2aof, 2aog, 2aoh, 3mim, 3d3t – HIVP (mutant) + substrate peptide
    
  • 4qj2, 4qj6, 4qj7, 4qj8, 4qj9, 4qja, 4fl8, 4flg, 4fm6, 4e43, 3b7v, 3b80, 2nxd, 2nxl, 2nxm, 4gzf – HIVP (mutant) + peptide
    
  • 1zsr, 1hbv – HIVP + peptidomimetic inhibitor
    
  • 1lzq, 1z8c, 1zbg, 1zj7, 1zpk – HIVP (mutant) + peptidomimetic inhibitor
    

• Drug resistant HIV-I protease

• • 4z4x, 4z50, 5t2e, 4q1w, 4q1x, 4q1y, 4qlh, 4nkk, 3uf3, 2avm, 2avo, 2avq, 2avs, 2avv, 3oq7, 3oqa, 3oqd, 3pj6, 1rpi, 1rq9, 1tw7 – HIVP (mutant)
    
  • 4ye3, 4yhq, 4rvi, 4rvx, 4njs, 4j54, 4j55, 3t3c, 3r0w, 3r0y, 2p3a, 2p3b, 2p3c, 2p3d, 1bv7, 1hvs, 1n49 – HIVP (mutant) + inhibitor
    
  • 4rvj – HIVP + drug
    
  • 5t2z, 4l1a, 4njt, 4nju, 4njv, 4j5j, 4eyr, 3ttp, 3ucb, 3ufn, 3u7s, 3uhl, 3ekp, 3ekq, 3ekt, 3ekv, 3ekw, 3eky, 3el0, 3el5, 3el9, 3em3, 3em4, 3em6, 1rv7, 1t7j, 3ggu – HIVP (mutant) + drug
    
  • 4obd, 4obf, 4obg, 4obh, 4obj, 4obk – HIVP (mutant) + peptide
    
  • 1fej, 1ff0, 1fff, 1ffi, 1fg6, 1fg8, 1fgc – HIVP (mutant) + substrate analog
    

• HIV-I protease complex at the top of the flap

• • 4ej8, 4ejl – HIVP (mutant) + indole derivative
    
  • 4k4q – HIVP (mutant) + bromobenzoate derivative
    
  • 4k4r – HIVP (mutant) + bromonaphthoate derivative
    
  • 4ejd, 4ejk – HIVP + pepstatin peptide + indole derivative
    
  • 4tvh – HIVP + inhibitor + indole derivative
    

• Synthetic HIV-I protease

• • 2o40 – syHIVP - synthetic
    
  • 3hau, 3haw, 3nwq, 3nwx, 3nxe, 3nxn, 3nyg, 4hvp – syHIVP + inhibitor
    
  • 3hlo, 3ia9, 3fsm, 3gi0, 3iaw, 3ka2, 3i2l, 7hvp, 8hvp – syHIVP (mutant) + inhibitor
    

• HIV-II

• • 3ebz – HIVP + drug
    
  • 3ec0, 3ecg, 1ida, 1idb, 3ec0, 3ecg, 1ivq – HIVP + inhibitor
    
  • 3upj, 4upj, 1ivp – HIVP (mutant) + inhibitor
    

• FIV

• • 1b11, 5fiv, 6fiv, 4fiv, 2fiv, 3fiv, 1fiv, 3tlh – FIVP + inhibitor – cat immunodeficiency virus
    
  • 2hah – FIVP (mutant) + inhibitor
    
  • 3ogp, 3ogq – FIVP (mutant) + drug
    

• SIV

• • 1sip – SIVP – monkey immunodeficiency virus
    
  • 1az5 – SIVP (mutant)
    
  • 1tcw, 2sam, 1siv – SIVP + inhibitor
    
  • 1ytg, 1yth, 1yti, 1ytj – SIVP + peptide
    

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Additional Resources

For additional information, see:

• Human Immunodeficiency Virus
• Structural Biology of HIV, an interactive Flash graphic of the virion with explanations of its components.

References

1. ↑ Wlodawer A, Miller M, Jaskolski M, Sathyanarayana BK, Baldwin E, Weber IT, Selk LM, Clawson L, Schneider J, Kent SB. Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science. 1989 Aug 11;245(4918):616-21. PMID:2548279
2. ↑ Lapatto R, Blundell T, Hemmings A, Overington J, Wilderspin A, Wood S, Merson JR, Whittle PJ, Danley DE, Geoghegan KF, et al.. X-ray analysis of HIV-1 proteinase at 2.7 A resolution confirms structural homology among retroviral enzymes. Nature. 1989 Nov 16;342(6247):299-302. PMID:2682266 doi:http://dx.doi.org/10.1038/342299a0
3. ↑ Tie Y, Kovalevsky AY, Boross P, Wang YF, Ghosh AK, Tozser J, Harrison RW, Weber IT. Atomic resolution crystal structures of HIV-1 protease and mutants V82A and I84V with saquinavir. Proteins. 2007 Apr 1;67(1):232-42. PMID:17243183 doi:10.1002/prot.21304
4. ↑ Maschera B, Darby G, Palu G, Wright LL, Tisdale M, Myers R, Blair ED, Furfine ES. Human immunodeficiency virus. Mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex. J Biol Chem. 1996 Dec 27;271(52):33231-5. PMID:8969180
5. ↑ Naicker P, Achilonu I, Fanucchi S, Fernandes M, Ibrahim MA, Dirr HW, Soliman ME, Sayed Y. Structural insights into the South African HIV-1 subtype C protease: impact of hinge region dynamics and flap flexibility in drug resistance. J Biomol Struct Dyn. 2012 Nov 12. PMID:23140382 doi:10.1080/07391102.2012.736774