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(-) Description

Title :  CRYSTAL STRUCTURES OF RECOMBINANT RAT CATHEPSIN B AND A CATHEPSIN B-INHIBITOR COMPLEX: IMPLICATIONS FOR STRUCTURE-BASED INHIBITOR DESIGN
 
Authors :  C. P. Huber, Z. Jia
Date :  03 May 95  (Deposition) - 31 Jul 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Jia, S. Hasnain, T. Hirama, X. Lee, J. S. Mort, R. To, C. P. Huber
Crystal Structures Of Recombinant Rat Cathepsin B And A Cathepsin B-Inhibitor Complex. Implications For Structure-Based Inhibitor Design.
J. Biol. Chem. V. 270 5527 1995
PubMed-ID: 7890671  |  Reference-DOI: 10.1074/JBC.270.10.5527
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CATHEPSIN B
    ChainsA, B
    EC Number3.4.22.1
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System CommonBAKER'S YEAST
    Expression System Taxid4932
    Expression System Vector TypePLASMID
    GeneCDNA
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PYS2Ligand/Ion2-PYRIDINETHIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:23 , CYS A:29 , PHE A:180 , HIS A:199 , ALA A:200 , ILE A:201 , ASN A:219 , TRP A:221BINDING SITE FOR RESIDUE PYS A 255
2AC2SOFTWAREGLN B:23 , CYS B:29 , PHE B:174 , VAL B:176 , HIS B:199 , ALA B:200 , ILE B:201 , ASN B:219 , TRP B:221 , HOH B:757BINDING SITE FOR RESIDUE PYS B 255
3ACTAUTHORCYS A:29 , HIS A:199 , ASN A:219ACTIVE SITE RESIDUES FOR RAT CATHEPSIN B IN CHAIN A
4BCTAUTHORCYS B:29 , HIS B:199 , ASN B:219ACTIVE SITE RESIDUES FOR RAT CATHEPSIN B IN CHAIN B

(-) SS Bonds  (12, 12)

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
7B:14 -B:43
8B:26 -B:71
9B:62 -B:128
10B:63 -B:67
11B:100 -B:132
12B:108 -B:119

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CTE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CATB_RAT_001 *V302ACATB_RAT  ---  ---A/BA223A
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.CATB_RAT102-113
 
  2A:23-34
B:23-34
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.CATB_RAT276-286
 
  2A:197-207
B:197-207
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.CATB_RAT293-312
 
  2A:214-233
B:214-233

(-) Exons   (0, 0)

(no "Exon" information available for 1CTE)

(-) 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:253
 aligned with CATB_RAT | P00787 from UniProtKB/Swiss-Prot  Length:339

    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_RAT    80 LPESFDAREQWSNCPTIAQIRDQGSCGSCWAFGAVEAMSDRICIHTNGRVNVEVSAEDLLTCCGIQCGDGCNGGYPSGAWNFWTRKGLVSGGVYNSHIGCLPYTIPPCEHHVNGSRPPCTGEGDTPKCNKMCEAGYSTSYKEDKHYGYTSYSVSDSEKEIMAEIYKNGPVEGAFTVFSDFLTYKSGVYKHEAGDVMGGHAIRILGWGIENGVPYWLVANSWNVDWGDNGFFKILRGENHCGIESEIVAGIPRT 332
               SCOP domains d1ctea_ A: (Pro)cathepsin B                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1cteA00 A:1-253 Cysteine proteinases                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ....eee.....................hhhhhhhhhhhhhhhhh..........hhhhhhh.............hhhhhhhhhh............................................................eeeeeeee...hhhhhhhhhhh..--------hhh.............eeeeeeeeeeeeeeee..eeeeeeee.........eeeeeee..........eeeeeee. Sec.struct. author (1)
     Sec.struct. author (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------eeeeeeeee--------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------ SAPs(SNPs)
                    PROSITE ----------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  -------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cte A   1 LPESFDAREQWSNCPTIAQIRDQGSCGSCWAFGAVEAMSDRICIHTNGRVNVEVSAEDLLTCCGIQCGDGCNGGYPSGAWNFWTRKGLVSGGVYNSHIGCLPYTIPPCEHHVNGARPPCTGEGDTPKCNKMCEAGYSTSYKEDKHYGYTSYSVSDSEKEIMAEIYKNGPVEGAFTVFSDFLTYKSGVYKHEAGDVMGGHAIRILGWGIENGVPYWLVANSWNADWGDNGFFKILRGENHCGIESEIVAGIPRT 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   

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with CATB_RAT | P00787 from UniProtKB/Swiss-Prot  Length:339

    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_RAT    80 LPESFDAREQWSNCPTIAQIRDQGSCGSCWAFGAVEAMSDRICIHTNGRVNVEVSAEDLLTCCGIQCGDGCNGGYPSGAWNFWTRKGLVSGGVYNSHIGCLPYTIPPCEHHVNGSRPPCTGEGDTPKCNKMCEAGYSTSYKEDKHYGYTSYSVSDSEKEIMAEIYKNGPVEGAFTVFSDFLTYKSGVYKHEAGDVMGGHAIRILGWGIENGVPYWLVANSWNVDWGDNGFFKILRGENHCGIESEIVAGIPRT 332
               SCOP domains d1cteb_ B: (Pro)cathepsin B                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1cteB00 B:1-253 Cysteine proteinases                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.....................hhhhhhhhhhhhhhhhh..........hhhhhhh.............hhhhhhhhhh............................................................eeeeeeee...hhhhhhhhhhh..eeeeeeeee...............eeeeeeeeeeeeeeee..eeeeeeee.........eeeeeee..........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------ SAPs(SNPs)
                    PROSITE ----------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  -------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cte B   1 LPESFDAREQWSNCPTIAQIRDQGSCGSCWAFGAVEAMSDRICIHTNGRVNVEVSAEDLLTCCGIQCGDGCNGGYPSGAWNFWTRKGLVSGGVYNSHIGCLPYTIPPCEHHVNGARPPCTGEGDTPKCNKMCEAGYSTSYKEDKHYGYTSYSVSDSEKEIMAEIYKNGPVEGAFTVFSDFLTYKSGVYKHEAGDVMGGHAIRILGWGIENGVPYWLVANSWNADWGDNGFFKILRGENHCGIESEIVAGIPRT 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   

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CTE)

(-) Gene Ontology  (39, 39)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CATB_RAT | P00787)
molecular function
    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:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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:0030984    kininogen binding    Interacting selectively and non-covalently with a kininogen, any of a group of plasma proteins that are kinin precursors.
    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:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
biological process
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0071260    cellular response to mechanical stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    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:0014075    response to amine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups.
    GO:0034097    response to cytokine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
    GO:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0009749    response to glucose    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus.
    GO:0070670    response to interleukin-4    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-4 stimulus.
    GO:0009612    response to mechanical stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0043434    response to peptide hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0007519    skeletal muscle tissue development    The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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: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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CATB_RAT | P007871cpj 1mir 1the

(-) Related Entries Specified in the PDB File

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