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(-) Description

Title :  A DUAL INHIBITOR OF THE LEUKOCYTE PROTEASES CATHEPSIN G AND CHYMASE WITH THERAPEUTIC EFFICACY IN ANIMALS MODELS OF INFLAMMATION
 
Authors :  L. De Garavilla, M. N. Greco, E. C. Giardino, G. I. Wells, B. J. Haertlein, J. A. Kauffman, T. W. Corcoran, C. K. Derian, A. J. Eckardt, W. M. Abraham, N. Sukumar, Z. Chen, A. O. Pineda, F. S. Mathews, E. Di Cera, P. Andrade-Gordon, B. P. Damiano, B. E. Maryanoff
Date :  23 Apr 04  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Inflammation Inhibitor Serine Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. De Garavilla, M. N. Greco, N. Sukumar, Z. W. Chen, A. O. Pineda, F. S. Mathews, E. Di Cera, E. C. Giardino, G. I. Wells, B. J. Haertlein, J. A. Kauffman, T. W. Corcoran, C. K. Derian, A. J. Eckardt, B. P. Damiano, P. Andrade-Gordon, B. E. Maryanoff
A Novel, Potent Dual Inhibitor Of The Leukocyte Proteases Cathepsin G And Chymase: Molecular Mechanisms And Anti-Inflammatory Activity In Vivo.
J. Biol. Chem. V. 280 18001 2005
PubMed-ID: 15741158  |  Reference-DOI: 10.1074/JBC.M501302200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CATHEPSIN G
    ChainsA
    EC Number3.4.21.20
    EngineeredYES
    GeneHUMAN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1OHH1Ligand/Ion2-[3-({METHYL[1-(2-NAPHTHOYL)PIPERIDIN-4-YL]AMINO}CARBONYL)-2-NAPHTHYL]-1-(1-NAPHTHYL)-2-OXOETHYLPHOSPHONIC ACID
2SO45Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:20 , GLU A:21 , ARG A:114 , ASN A:119 , ARG A:156 , HOH A:1045 , HOH A:1078 , HOH A:1127 , HOH A:1201BINDING SITE FOR RESIDUE SO4 A 902
2AC2SOFTWAREARG A:170 , ARG A:178 , ARG A:179 , LYS A:217 , HOH A:1232BINDING SITE FOR RESIDUE SO4 A 903
3AC3SOFTWAREARG A:75 , ARG A:76BINDING SITE FOR RESIDUE SO4 A 904
4AC4SOFTWAREARG A:86 , ARG A:97 , GLN A:107 , PRO A:132 , ARG A:147 , HOH A:1200BINDING SITE FOR RESIDUE SO4 A 905
5AC5SOFTWAREARG A:86 , ARG A:131 , SER A:145 , MET A:146 , ARG A:147 , HOH A:1094 , HOH A:1211BINDING SITE FOR RESIDUE SO4 A 906
6AC6SOFTWAREHIS A:57 , ILE A:99 , ARG A:166 , LEU A:169 , PHE A:172 , ASP A:176 , PRO A:177 , ARG A:178 , ALA A:190 , LYS A:192 , GLY A:193 , SER A:195 , SER A:214 , TYR A:215 , GLY A:216 , LYS A:217 , SER A:218 , GLU A:226 , HOH A:1063 , HOH A:1087 , HOH A:1110 , HOH A:1130 , HOH A:1137BINDING SITE FOR RESIDUE OHH A 901

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:224 -Pro A:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_006491N125SCATG_HUMANPolymorphism45567233AN119S

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CATG_HUMAN21-243  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CATG_HUMAN60-65  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CATG_HUMAN195-206  1A:189-200

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002163361ENSE00000889480chr14:25045466-2504537592CATG_HUMAN1-19190--
1.2ENST000002163362ENSE00000654531chr14:25044618-25044471148CATG_HUMAN19-68501A:16-6148
1.3ENST000002163363ENSE00000654530chr14:25044016-25043881136CATG_HUMAN68-113461A:61-107 (gaps)47
1.4ENST000002163364ENSE00000654529chr14:25043705-25043451255CATG_HUMAN114-198851A:108-192 (gaps)87
1.5ENST000002163365ENSE00001267767chr14:25043016-25042762255CATG_HUMAN199-255571A:193-244 (gaps)52

(-) 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:224
 aligned with CATG_HUMAN | P08311 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:224
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
          CATG_HUMAN     21 IIGGRESRPHSRPYMAYLQIQSPAGQSRCGGFLVREDFVLTAAHCWGSNINVTLGAHNIQRRENTQQHITARRAIRHPQYNQRTIQNDIMLLQLSRRVRRNRNVNPVALPRAQEGLRPGTLCTVAGWGRVSMRRGTDTLREVQLRVQRDRQCLRIFGSYDPRRQICVGDRRERKAAFKGDSGGPLLCNNVAHGIVSYGKSSGVPPEVFTRVSSFLPWIRTTMRS  244
               SCOP domains d1t32a_ A: Urokinase-type plasminogen activator (LMW U-PA), catalytic domain                                                                                                                                                     SCOP domains
               CATH domains 1t32A01     1t32A02 A:28-120,A:233-244 Trypsin-like serine proteases                                      1t32A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                   1t32A02      CATH domains
               Pfam domains Trypsin-1t32A01 A:16-238                                                                                                                                                                                                  ------ Pfam domains
         Sec.struct. author ....ee........eeeeee.......eeeeeeee..eeeehhhhh...eeeee............eeeeeeeeee.............eeeee..........................eeeeee.............eeeeee..hhhhhhhhh.......eeee................eeee..eeeeeeee........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------S----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 21-243                                                                                                                                                                                     - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-61 UniProt: 19-68           ---------------------------------------------Exon 1.4  PDB: A:108-192 (gaps) UniProt: 114-198                                     Exon 1.5  PDB: A:193-244 (gaps) [INCOMPLETE]   Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3  PDB: A:61-107 (gaps) UniProt: 68-113----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1t32 A   16 IIGGRESRPHSRPYMAYLQIQSPAGQSRCGGFLVREDFVLTAAHCWGSNINVTLGAHNIQRRENTQQHITARRAIRHPQYNQRTIQNDIMLLQLSRRVRRNRNVNPVALPRAQEGLRPGTLCTVAGWGRVSMRRGTDTLREVQLRVQRDRQCLRIFGSYDPRRQICVGDRRERKAAFKGDSGGPLLCNNVAHGIVSYGKSSGVPPEVFTRVSSFLPWIRTTMRS  244
                                    25        35 ||     43        53       |64        74        84        94       104       114       124       134       144   ||  156       166       176       185  |    194       204|      218  ||   230       240    
                                               36A|                       61|                                                                                  148|                             184A 188A              204|         221|                    
                                                36B                        63                                                                                   151                                                     209          224                    

   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, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CATG_HUMAN | P08311)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    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: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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0002003    angiotensin maturation    The process leading to the attainment of the full functional capacity of angiotensin by conversion of renin substrate into mature angiotensin in the blood.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0050832    defense response to fungus    Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0044130    negative regulation of growth of symbiont in host    Any process in which the symbiont stops, prevents or reduces its increase in size or mass within the cells or tissues of the host organism. The host is defined as the larger of the organisms involved in the symbiotic interaction.
    GO:0070946    neutrophil mediated killing of gram-positive bacterium    The directed killing of a gram-positive bacterium by a neutrophil.
    GO:0050778    positive regulation of immune response    Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CATG_HUMAN | P083111au8 1cgh 1kyn

(-) Related Entries Specified in the PDB File

1cgh THE 1.8 A CRYSTAL STRUCTURE OF HUMAN CATHEPSIN G IN COMPLEX WITH SUC-VAL-PRO-PHEP-(OPH)2: A JANUS-FACED PROTEINASE WITH TWO OPPOSITE SPECIFICITIES