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Conserved domains on  [gi|2624747|pdb|2AID|A]
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Chain A, Structure Of A Non-Peptide Inhibitor Complexed With Hiv-1 Protease: Developing A Cycle Of Structure-Based Drug Design

Protein Classification

protease (domain architecture ID 10442194)

protease containing the pepsin-like aspartate protease domain such as HIV-1 protease and Avian myeloblastosis-associated virus proteinase p15, which specifically liberates the five major structural proteins from the common gag precursor, as well as reverse transcriptase and integrase from the gag-pol precursor

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
8-98 1.63e-30

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


:

Pssm-ID: 306563  Cd Length: 99  Bit Score: 103.57  E-value: 1.63e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AID_A         8 RPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKW----KPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTV--LVGP-T 80
Cdd:pfam00077  2 RPLLTVKIGGKPFTALLDTGADHTVISENDWPTNWpkqkATSWIQGIGGGINVRQSDQILILLGEDDFTGPVspLILPtC 81
                         90
                 ....*....|....*...
2AID_A        81 PVNIIGRNLLTQIGCTLN 98
Cdd:pfam00077 82 PVNIIGRDLLQQLGARLT 99
 
Name Accession Description Interval E-value
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
8-98 1.63e-30

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 306563  Cd Length: 99  Bit Score: 103.57  E-value: 1.63e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AID_A         8 RPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKW----KPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTV--LVGP-T 80
Cdd:pfam00077  2 RPLLTVKIGGKPFTALLDTGADHTVISENDWPTNWpkqkATSWIQGIGGGINVRQSDQILILLGEDDFTGPVspLILPtC 81
                         90
                 ....*....|....*...
2AID_A        81 PVNIIGRNLLTQIGCTLN 98
Cdd:pfam00077 82 PVNIIGRDLLQQLGARLT 99
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
11-91 1.61e-26

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 93.10  E-value: 1.61e-26
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AID_A      11 VTIRIGGQLKEALLDTGADDTVLEEMNLPGKW----KPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGP--TPVNI 84
Cdd:cd05482  1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80

               ....*..
2AID_A      85 IGRNLLT 91
Cdd:cd05482 81 WGRDILS 87
 
Name Accession Description Interval E-value
RVP pfam00077
Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, ...
8-98 1.63e-30

Retroviral aspartyl protease; Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026).


Pssm-ID: 306563  Cd Length: 99  Bit Score: 103.57  E-value: 1.63e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AID_A         8 RPLVTIRIGGQLKEALLDTGADDTVLEEMNLPGKW----KPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTV--LVGP-T 80
Cdd:pfam00077  2 RPLLTVKIGGKPFTALLDTGADHTVISENDWPTNWpkqkATSWIQGIGGGINVRQSDQILILLGEDDFTGPVspLILPtC 81
                         90
                 ....*....|....*...
2AID_A        81 PVNIIGRNLLTQIGCTLN 98
Cdd:pfam00077 82 PVNIIGRDLLQQLGARLT 99
HIV_retropepsin_like cd05482
Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family ...
11-91 1.61e-26

Retropepsins, pepsin-like aspartate proteases; This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133149  Cd Length: 87  Bit Score: 93.10  E-value: 1.61e-26
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AID_A      11 VTIRIGGQLKEALLDTGADDTVLEEMNLPGKW----KPKMIGGIGGFIKVRQYDQIPVEICGHKAIGTVLVGP--TPVNI 84
Cdd:cd05482  1 LTLYINGKLFEGLLDTGADVSIIAENDWPKNWpiqpAPSNLTGIGGAITPSQSSVLLLEIDGEGHLGTILVYVlsLPVNL 80

               ....*..
2AID_A      85 IGRNLLT 91
Cdd:cd05482 81 WGRDILS 87
RP_RTVL_H_like cd06095
Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family ...
11-91 9.22e-06

Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements; This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A.


Pssm-ID: 133159  Cd Length: 86  Bit Score: 40.01  E-value: 9.22e-06
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AID_A      11 VTIRIGGQLKEALLDTGADDTVLEEMNLPGKW---KPKMIGGIGGFIKVRQydQIPVEIC---GHKAIGTVLVGPT-PVN 83
Cdd:cd06095  1 VTITVEGVPIVFLVDTGATHSVLKSDLGPKQElstTSVLIRGVSGQSQQPV--TTYRTLVdlgGHTVSHSFLVVPNcPDP 78

               ....*...
2AID_A      84 IIGRNLLT 91
Cdd:cd06095 79 LLGRDLLS 86
Asp_protease_2 pfam13650
Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to ...
11-89 1.38e-03

Aspartyl protease; This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix.


Pssm-ID: 338873  Cd Length: 90  Bit Score: 34.58  E-value: 1.38e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AID_A        11 VTIRIGGQLKEALLDTGADDTVL-----EEMNLPGKWK--PKMIGGIGGFIKVRQYDQIPVEICGHKAIG-TVLVGPTPV 82
Cdd:pfam13650  1 VPVTINGKPVRFLLDTGASGTVIspslaERLGLKPDGLayTVRVSTAGGTVEAALVRLDSLRLGGLTLKNvPALVLDLGD 80
                         90
                 ....*....|
2AID_A        83 ---NIIGRNL 89
Cdd:pfam13650 81 lidGLLGMDF 90
gag-asp_proteas pfam13975
gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is ...
11-92 3.48e-03

gag-polyprotein putative aspartyl protease; This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins.


Pssm-ID: 339031  Cd Length: 92  Bit Score: 33.30  E-value: 3.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2AID_A        11 VTIRIGGQLKEALLDTGADDTVL-----EEMNLP--GKWKPKMIGGIGGFIKVRQY--DQIPV-EICGHKAIGTVLVGPT 80
Cdd:pfam13975  1 VDVTINGRPVKFLVDTGASSTVIsealaERLGLDrlVDAYPVTVRTANGTVRAARVrlDSVKIgGIELRNVPAVVLPGDL 80
                         90
                 ....*....|..
2AID_A        81 PVNIIGRNLLTQ 92
Cdd:pfam13975 81 DDVLLGMDFLKR 92
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.17
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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