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(-) Description

Title :  SECRETED ASPARTIC PROTEASE IN COMPLEX WITH RITONAVIR
 
Authors :  H. Koester, A. Heine, G. Klebe
Date :  04 Jan 11  (Deposition) - 04 Jan 12  (Release) - 04 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Koester, A. Heine, G. Klebe
The Bindingmode Of Hiv-1 Protease Inhibitors To Pepsin-Like Aspartic Proteinases
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CANDIDAPEPSIN-2
    Chains: A
    EC Number: 3.4.23.24
    Fragment: UNP RESIDUES 57-398
    Organism Common: YEAST
    Organism Scientific: CANDIDA ALBICANS
    Organism Taxid: 5476
    Synonym: ACP 2, ASPARTATE PROTEASE 2, SECRETED ASPARTIC PROTEASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
2RIT1Ligand/IonRITONAVIR
3ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:32 , GLY A:34 , SER A:35 , GLY A:83 , TYR A:84 , GLY A:85 , ILE A:119 , ASP A:120 , ASN A:131 , ASP A:218 , GLY A:220 , THR A:221 , THR A:222 , TYR A:225 , ILE A:305 , HOH A:6004 , HOH A:6106 , HOH A:6173BINDING SITE FOR RESIDUE RIT A 2001
2AC2SOFTWAREASP A:57 , GLU A:324 , HOH A:6195 , HOH A:6204BINDING SITE FOR RESIDUE ZN A 3000
3AC3SOFTWAREHOH A:6196 , HOH A:6199 , HOH A:6200 , HOH A:6201 , HOH A:6202BINDING SITE FOR RESIDUE ZN A 3001
4AC4SOFTWARELEU A:183 , SER A:326 , HOH A:6024 , HOH A:6058 , HOH A:6137BINDING SITE FOR RESIDUE MRD A 4001

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:47 -A:59
2A:256 -A:294

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3Q70)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CARP2_CANAL_002 *V273LCARP2_CANAL  ---  ---AL217L
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.CARP2_CANAL70-384  1A:14-328
CARP2_CANAW70-384  1A:14-328
CARP2_CANAX70-384  1A:14-328
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.CARP2_CANAL85-96
271-282		  2A:29-40
A:215-226
CARP2_CANAW85-96
271-282		  2A:29-40
A:215-226
CARP2_CANAX85-96
271-282		  2A:29-40
A:215-226

(-) Exons   (0, 0)

(no "Exon" information available for 3Q70)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:334
 aligned with CARP2_CANAL | P0DJ06 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:342
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396  
          CARP2_CANAL    57 QAVPVTLHNEQVTYAADITVGSNNQKLNVIVDTGSSDLWVPDVNVDCQVTYSDQTADFCKQKGTYDPSGSSASQDLNTPFKIGYGDGSSSQGTLYKDTVGFGGVSIKNQVLADVDSTSIDQGILGVGYKTNEAGGSYDNVPVTLKKQGVIAKNAYSLYLNSPDAATGQIIFGGVDNAKYSGSLIALPVTSDRELRISLGSVEVSGKTINTDNVDVLVDSGTTITYLQQDLADQIIKAFNGKLTQDSNGNSFYEVDCNLSGDVVFNFSKNAKISVPASEFAASLQGDDGQPYDKCQLLFDVNDANILGDNFLRSAYIVYDLDDNEISLAQVKYTSASSISALT 398
               SCOP domains d3q70a_ A: Acid protease                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....eeeeeeee.....eeeeeeeeee.........hhhhh....hhhhh...eeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeeeeee.....eee..hhhhh......hhhhhhhhh......eeeee.......eeeeee.eee........eeee.......eeeeeeeee..eeeeeeeeeeee......eeehhhhhhhhhhhh..eeee.....eeeeee.....eeeee.....eeeee....ee..--------.eeee.eee....eehhhhhh.eeeeee....eeeeee........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) -------------PEPTIDASE_A1  PDB: A:14-328 UniProt: 70-384                                                                                                                                                                                                                                                                                -------------- PROSITE (3)
                PROSITE (4) ----------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q70 A   1 QAVPVTLHNEQVTYAADITVGSNNQKLNVIVDTGSSDLWVPDVNVDCQVTYSDQTADFCKQKGTYDPSGSSASQDLNTPFKIGYGDGSSSQGTLYKDTVGFGGVSIKNQVLADVDSTSIDQGILGVGYKTNEAGGSYDNVPVTLKKQGVIAKNAYSLYLNSPDAATGQIIFGGVDNAKYSGSLIALPVTSDRELRISLGSVEVSGKTINTDNVDVLLDSGTTITYLQQDLADQIIKAFNGKLTQDSNGNSFYEVDCNLSGDVVFNFSKNAKISVPASEFAASL--------DKCQLLFDVNDANILGDNFLRSAYIVYDLDDNEISLAQVKYTSASSISALT 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  |      - |     300       310       320       330       340  
                                                                                                                                                                                                                                                                                                                    283      292                                                  


Chain A from PDB  Type:PROTEIN  Length:334
 aligned with CARP2_CANAW | C4YMJ3 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:342
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396  
          CARP2_CANAW    57 QAVPVTLHNEQVTYAADITVGSNNQKLNVIVDTGSSDLWVPDVNVDCQVTYSDQTADFCKQKGTYDPSGSSASQDLNTPFKIGYGDGSSSQGTLYKDTVGFGGVSIKNQVLADVDSTSIDQGILGVGYKTNEAGGSYDNVPVTLKKQGVIAKNAYSLYLNSPDAATGQIIFGGVDNAKYSGSLIALPVTSDRELRISLGSVEVSGKTINTDNVDVLLDSGTTITYLQQDLADQIIKAFNGKLTQDSNGNSFYEVDCNLSGDVVFNFSKNAKISVPASEFAASLQGDDGQPYDKCQLLFDVNDANILGDNFLRSAYIVYDLDNNEISLAQVKYTSASSISALT 398
               SCOP domains d3q70a_ A: Acid protease                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....eeeeeeee.....eeeeeeeeee.........hhhhh....hhhhh...eeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeeeeee.....eee..hhhhh......hhhhhhhhh......eeeee.......eeeeee.eee........eeee.......eeeeeeeee..eeeeeeeeeeee......eeehhhhhhhhhhhh..eeee.....eeeeee.....eeeee.....eeeee....ee..--------.eeee.eee....eehhhhhh.eeeeee....eeeeee........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------PEPTIDASE_A1  PDB: A:14-328 UniProt: 70-384                                                                                                                                                                                                                                                                                -------------- PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (4)
                PROSITE (5) ----------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------- PROSITE (5)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q70 A   1 QAVPVTLHNEQVTYAADITVGSNNQKLNVIVDTGSSDLWVPDVNVDCQVTYSDQTADFCKQKGTYDPSGSSASQDLNTPFKIGYGDGSSSQGTLYKDTVGFGGVSIKNQVLADVDSTSIDQGILGVGYKTNEAGGSYDNVPVTLKKQGVIAKNAYSLYLNSPDAATGQIIFGGVDNAKYSGSLIALPVTSDRELRISLGSVEVSGKTINTDNVDVLLDSGTTITYLQQDLADQIIKAFNGKLTQDSNGNSFYEVDCNLSGDVVFNFSKNAKISVPASEFAASL--------DKCQLLFDVNDANILGDNFLRSAYIVYDLDDNEISLAQVKYTSASSISALT 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  |      - |     300       310       320       330       340  
                                                                                                                                                                                                                                                                                                                    283      292                                                  


Chain A from PDB  Type:PROTEIN  Length:334
 aligned with CARP2_CANAX | P0CS83 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:342
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396  
          CARP2_CANAX    57 QAVPVTLHNEQVTYAADITVGSNNQKLNVIVDTGSSDLWVPDVNVDCQVTYSDQTADFCKQKGTYDPSGSSASQDLNTPFKIGYGDGSSSQGTLYKDTVGFGGVSIKNQVLADVDSTSIDQGILGVGYKTNEAGGSYDNVPVTLKKQGVIAKNAYSLYLNSPDAATGQIIFGGVDNAKYSGSLIALPVTSDRELRISLGSVEVSGKTINTDNVDVLLDSGTTITYLQQDLADQIIKAFNGKLTQDSNGNSFYEVDCNLSGDVVFNFSKNAKISVPASEFAASLQGDDGQPYDKCQLLFDVNDANILGDNFLRSAYIVYDLDDNEISLAQVKYTSASSISALT 398
               SCOP domains d3q70a_ A: Acid protease                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....eeeeeeee.....eeeeeeeeee.........hhhhh....hhhhh...eeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeeeeee.....eee..hhhhh......hhhhhhhhh......eeeee.......eeeeee.eee........eeee.......eeeeeeeee..eeeeeeeeeeee......eeehhhhhhhhhhhh..eeee.....eeeeee.....eeeee.....eeeee....ee..--------.eeee.eee....eehhhhhh.eeeeee....eeeeee........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------PEPTIDASE_A1  PDB: A:14-328 UniProt: 70-384                                                                                                                                                                                                                                                                                -------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (3)
                PROSITE (4) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (4)
                PROSITE (5) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (5)
                PROSITE (6) ----------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------- PROSITE (6)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3q70 A   1 QAVPVTLHNEQVTYAADITVGSNNQKLNVIVDTGSSDLWVPDVNVDCQVTYSDQTADFCKQKGTYDPSGSSASQDLNTPFKIGYGDGSSSQGTLYKDTVGFGGVSIKNQVLADVDSTSIDQGILGVGYKTNEAGGSYDNVPVTLKKQGVIAKNAYSLYLNSPDAATGQIIFGGVDNAKYSGSLIALPVTSDRELRISLGSVEVSGKTINTDNVDVLLDSGTTITYLQQDLADQIIKAFNGKLTQDSNGNSFYEVDCNLSGDVVFNFSKNAKISVPASEFAASL--------DKCQLLFDVNDANILGDNFLRSAYIVYDLDDNEISLAQVKYTSASSISALT 342
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  |      - |     300       310       320       330       340  
                                                                                                                                                                                                                                                                                                                    283      292
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q70)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3Q70)

(-) Gene Ontology  (15, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CARP2_CANAX | P0CS83)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A   (CARP2_CANAW | C4YMJ3)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A   (CARP2_CANAL | P0DJ06)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0044406    adhesion of symbiont to host    The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044257    cellular protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
    GO:0052391    induction by symbiont of defense-related host calcium ion flux    The activation by an organism of a flux of calcium ions that occurs as part of the defense response of a host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044416    induction by symbiont of host defense response    The activation by an organism of the defense response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0019538    protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006465    signal peptide processing    The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  3q70
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  CARP2_CANAX | P0CS83
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  3.4.23.24
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CARP2_CANAL | P0DJ06: 1eag 1zap 3pvk
        CARP2_CANAW | C4YMJ3: 1eag 1zap 3pvk
        CARP2_CANAX | P0CS83: 1eag 1zap 3pvk

(-) Related Entries Specified in the PDB File

3prs ENDOTHIAPEPSIN IN COMPLEX WITH RITONAVIR
3pww ENDOTHIAPEPSIN IN COMPLEX WITH SAQUINAVIR