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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE ANALYSIS OF BOVINE SPLEEN CATHEPSIN B-CA042 COMPLEX
 
Authors :  D. Watanabe
Date :  31 Dec 05  (Deposition) - 24 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A
Keywords :  Cathepsin B, Cysteine Protease, Ca042, Hydrolase, Ec 3. 4. 22. 1 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Watanabe, A. Yamamoto, K. Matsumoto, M. Murata, K. Kitamura, K. Tomoo, T. Ishida
Quantitative Estimation Of Each Active Subsite Of Cathepsin B For The Inhibitory Activity, Based On The Inhibitory Activitybinding Mode Relationship Of A Series Of Epoxysuccinyl Inhibitors By X-Ray Crystal Structure Analyse Of The Complexes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CATHEPSIN B
    ChainsA
    EC Number3.4.22.1
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    TissueSPLEEN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
10421Ligand/IonN-{[(2S,3S)-3-(ETHOXYCARBONYL)OXIRAN-2-YL]CARBONYL}-L-THREONYL-L-ISOLEUCINE
2GOL1Ligand/IonGLYCEROL
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:2 , GLN A:10 , SER A:129 , TYR A:165 , HOH A:843 , HOH A:894 , HOH A:897 , HOH A:941BINDING SITE FOR RESIDUE PO4 A 801
2AC2SOFTWAREGLN A:23 , GLY A:24 , GLY A:27 , SER A:28 , CYS A:29 , TRP A:30 , GLY A:73 , GLY A:74 , HIS A:110 , HIS A:111 , CYS A:119 , GLY A:198 , HIS A:199 , TRP A:221 , HOH A:927 , HOH A:1006BINDING SITE FOR RESIDUE 042 A 420
3AC3SOFTWAREARG A:8 , ASP A:227 , ASN A:228 , LYS A:232 , HOH A:988BINDING SITE FOR RESIDUE GOL A 500

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:14 -A:43
2A:26 -A:71
3A:62 -A:128
4A:63 -A:67
5A:100 -A:132
6A:108 -A:119
7A:148 -A:252

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:137 -Pro A:138

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DC7)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATB_BOVIN102-113  1A:23-34
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATB_BOVIN276-286  1A:197-207
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATB_BOVIN293-312  1A:214-233

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENSBTAT000000367952bENSBTAE00000134363chr8:7457578-7457703126CATB_BOVIN1-42420--
1.3ENSBTAT000000367953ENSBTAE00000134364chr8:7458358-745844386CATB_BOVIN43-71290--
1.4ENSBTAT000000367954ENSBTAE00000134365chr8:7459328-7459442115CATB_BOVIN71-109391A:1-3030
1.5ENSBTAT000000367955ENSBTAE00000134366chr8:7461238-7461356119CATB_BOVIN110-149401A:31-70 (gaps)40
1.6ENSBTAT000000367956ENSBTAE00000134368chr8:7462142-746222786CATB_BOVIN149-178301A:70-9930
1.7ENSBTAT000000367957ENSBTAE00000134369chr8:7462523-7462666144CATB_BOVIN178-226491A:99-14749
1.8ENSBTAT000000367958ENSBTAE00000134370chr8:7463058-7463174117CATB_BOVIN226-265401A:147-18640
1.9ENSBTAT000000367959ENSBTAE00000134371chr8:7464281-7464409129CATB_BOVIN265-308441A:186-22944
1.10bENSBTAT0000003679510bENSBTAE00000287995chr8:7465007-74660621056CATB_BOVIN308-335281A:229-25325

(-) 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:251
 aligned with CATB_BOVIN | P07688 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:253
                                    89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329   
           CATB_BOVIN    80 LPESFDAREQWPNCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHSNGRVNVEVSAEDMLTCCGGECGDGCNGGFPSGAWNFWTKKGLVSGGLYNSHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKTCEPGYSPSYKEDKHFGCSSYSVANNEKEIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVSGEIMGGHAIRILGWGVENGTPYWLVGNSWNTDWGDNGFFKILRGQDHCGIESEIVAGMPCT 332
               SCOP domains d2dc7a_ A: automated matches                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2dc7A00 A:1-253 Cysteine proteinases                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhh..hhhhhh........hhhhhhhhhhhhhhhhhh..--.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh............................................................eeeeeee..hhhhhhhhhhhhh.eeeeeeeehhhhh....ee......eeeeeeeeeeeeeee..eeeeeee...........eeeee...hhhhh...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  -------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:1-30         Exon 1.5  PDB: A:31-70 (gaps)           ----------------------------Exon 1.7  PDB: A:99-147 UniProt: 178-226         ---------------------------------------------------------------------------------Exon 1.10b  PDB: A:229-25 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------Exon 1.6  PDB: A:70-99        -----------------------------------------------Exon 1.8  PDB: A:147-186                ------------------------------------------------------------------- Transcript 1 (2)
           Transcript 1 (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:186-229 UniProt: 265-308   ------------------------ Transcript 1 (3)
                 2dc7 A   1 LPESFDAREQWPNCPTIKEIRDQGSCGSCWAFGAVEAISDRICIHSN--VNVEVSAEDMLTCCGGECGDGCNGGFPSGAWNFWTKKGLVSGGLYNSHVGCRPYSIPPCEHHVNGSRPPCTGEGDTPKCSKTCEPGYSPSYKEDKHFGCSSYSVANNEKEIMAEIYKNGPVEGAFSVYSDFLLYKSGVYQHVSGEIMGGHAIRILGWGVENGTPYWLVGNSWNTDWGDNGFFKILRGQDHCGIESEIVAGMPCT 253
                                    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   
                                                                         47 50                                                                                                                                                                                                           

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DC7)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CATB_BOVIN | P07688)
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: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:0097067    cellular response to thyroid hormone stimulus    A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus.
    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:0046697    decidualization    The cellular and vascular changes occurring in the endometrium of the pregnant uterus just after the onset of blastocyst implantation. This process involves the proliferation and differentiation of the fibroblast-like endometrial stromal cells into large, polyploid decidual cells that eventually form the maternal component of the placenta.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    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:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CATB_BOVIN | P076881ito 1qdq 1sp4 2dc6 2dc8 2dc9 2dca 2dcb 2dcc 2dcd

(-) Related Entries Specified in the PDB File

1ito THE SAME PROTEIN COMPLEXED WITH E64C
1qdq THE SAME PROTEIN COMPLEXED WITH CA074
2dc6 THE SAME PROTEIN COMPLEXED WITH CA073
2dc8 THE SAME PROTEIN COMPLEXED WITH CA059
2dc9 THE SAME PROTEIN COMPLEXED WITH CA074ME
2dca THE SAME PROTEIN COMPLEXED WITH CA075
2dcb THE SAME PROTEIN COMPLEXED WITH CA076
2dcc THE SAME PROTEIN COMPLEXED WITH CA077
2dcd THE SAME PROTEIN COMPLEXED WITH CA078