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(-) Description

Title :  A MUTANT RABBIT CATHEPSIN K WITH A NITRILE INHIBITOR
 
Authors :  J. R. Somoza
Date :  30 Nov 05  (Deposition) - 07 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Papain Cysteine Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. N. Crane, W. C. Black, J. T. Palmer, D. E. Davis, E. Setti, J. Robichaud, J. Paquet, R. M. Oballa, C. I. Bayly, D. J. Mckay, J. R. Somoza, N. Chauret, C. Seto, J. Scheigetz, G. Wesolowski, F. Masse, S. Desmarais, M. Ouellet
Beta-Substituted Cyclohexanecarboxamide: A Nonpeptidic Framework For The Design Of Potent Inhibitors Of Cathepsin K.
J. Med. Chem. V. 49 1066 2006
PubMed-ID: 16451072  |  Reference-DOI: 10.1021/JM051059P
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CATHEPSIN K
    ChainsA
    EC Number3.4.22.38
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    GeneCTSK
    MutationYES
    Organism CommonRABBIT
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986
    SynonymOC-2 PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NOQ1Ligand/Ion(1R,2R)-N-(2-AMINOETHYL)-2-{[(4-METHOXYPHENYL)SULFONYL]METHYL}CYCLOHEXANECARBOXAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:4 , GLN A:19 , GLY A:23 , CYS A:25 , GLU A:59 , ASN A:60 , GLY A:65 , GLY A:66 , TYR A:67 , ASN A:158BINDING SITE FOR RESIDUE NOQ A 600

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:63
2A:56 -A:95
3A:153 -A:200

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F7D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F7D)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATK_RABIT133-144  1A:19-30
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATK_RABIT274-284  1A:158-167
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATK_RABIT291-310  1A:170-189

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSOCUT000000110871ENSOCUE00000277601chr13:41346878-4134690023CATK_RABIT-00--
1.2ENSOCUT000000110872ENSOCUE00000129231chr13:41348343-41348463121CATK_RABIT1-40400--
1.3ENSOCUT000000110873ENSOCUE00000129237chr13:41349905-41350027123CATK_RABIT41-81410--
1.4ENSOCUT000000110874ENSOCUE00000129248chr13:41350114-41350269156CATK_RABIT82-133521A:1-1919
1.5ENSOCUT000000110875ENSOCUE00000129255chr13:41351252-41351470219CATK_RABIT134-206731A:20-9173
1.6ENSOCUT000000110876ENSOCUE00000129266chr13:41357620-41357785166CATK_RABIT207-262561A:92-147 (gaps)57
1.7ENSOCUT000000110877ENSOCUE00000129271chr13:41358011-41358116106CATK_RABIT262-297361A:147-17636
1.8ENSOCUT000000110878ENSOCUE00000129278chr13:41359590-41360274685CATK_RABIT297-329331A:176-211 (gaps)36

(-) 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:215
 aligned with CATK_RABIT | P43236 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:215
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
          CATK_RABIT    115 TPDSIDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENYGCGGGYMTNAFQYVQRNRGIDSEDAYPYVGQDESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDENCSSDNVNHAVLAVGYGIQKGNKHWIIKNSWGESWGNKGYILMARNKNNACGIANLASFPKM  329
               SCOP domains d2f7da1 A:1-211 (Pro)cathepsin K                                                                                                                                                                                        SCOP domains
               CATH domains 2f7dA00 A:1-211 Cysteine proteinases                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh.ee.hhhh...........hhh.eee....eee....hhhhhhhhhhhh..eeeee...hhhhhh....ee...........eeeeeeeeeee..eeeeeee...........eeeee....hhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA---------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------- PROSITE
           Transcript 1 (1) Exon 1.4           Exon 1.5  PDB: A:20-91 UniProt: 134-206                                  Exon 1.6  PDB: A:92-147 (gaps) UniProt: 207-262         ----------------------------------Exon 1.8  PDB: A:176-211 (gaps)   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:147-176            -------------------------------- Transcript 1 (2)
                2f7d A    1 TPDSIDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQLKKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQRNRGIDSEDAYPYVGQDESCMYNPTGKAAKCRGYREIPEGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDENCSSDNLNHAVLAVGYGIQKGNKHWIIKNSWGESWGNKGYILMARNKNNACGIANLASFPKM  211
                                    10        20        30        40        50        60        70        79        89        99   ||  110       120       129       139       149 |     157       167 ||||  173       183       193||     206     
                                                                                                        78A                      103|                   127A                    150A   156A         168A|||                       194|             
                                                                                                                                  105                                                                168B||                        198             
                                                                                                                                                                                                      168C|                                        
                                                                                                                                                                                                       168D                                        

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  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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F7D)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CATK_RABIT | P43236)
molecular function
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0001968    fibronectin binding    Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids.
    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.
    GO:0043394    proteoglycan binding    Interacting selectively and non-covalently with a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
biological process
    GO:0030574    collagen catabolic process    The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
    GO:1903955    positive regulation of protein targeting to mitochondrion    Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051603    proteolysis involved in cellular protein catabolic process    The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
    GO:1903146    regulation of mitophagy    Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
cellular component
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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