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(-) Description

Title :  KNOWLEDGE BASED MODEL OF PROSTATE SPECIFIC ANTIGEN (THEORETICAL MODEL) BOUND TO A CONSENSUS PEPTIDE SUBSTRATE
 
Authors :  J. L. Pellequer
Date :  11 Mar 99  (Deposition) - 16 Mar 99  (Release) - 16 Mar 99  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A,I
Keywords :  Kallikrein, Serine Protease, Psa, Substrate Phage Display (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. S. Coombs, R. C. Bergstrom, J. L. Pellequer, S. I. Baker, M. Navre, M. M. Smith, J. A. Tainer, E. L. Madison, D. R. Corey
Substrate Specificity Of Prostate-Specific Antigen (Psa).
Chem. Biol. V. 5 475 1998
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PROSTATE SPECIFIC ANTIGEN)
    ChainsA
    EC Number3.4.21.77
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymPSA
 
Molecule 2 - PROTEIN (CONSENSUS PEPTIDE SUBSTRATE)
    ChainsI
    EngineeredYES
    Other DetailsHEXAPEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

Theoretical Model (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

Theoretical Model (1, 1)
No.NameEvidenceResiduesDescription
1CATnot definedHIS A:57 , ASP A:102 , SER A:195

(-) SS Bonds  (5, 5)

Theoretical Model
No.Residues
1A:22 -A:157
2A:42 -A:58
3A:136 -A:201
4A:168 -A:182
5A:191 -A:220

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Glu A:218 -Pro A:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Theoretical Model (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_021941E32KKLK3_HUMANPolymorphism2271092AE23K
2UniProtVAR_021942L132IKLK3_HUMANPolymorphism2003783AL114I
3UniProtVAR_051852I179TKLK3_HUMANPolymorphism17632542AI163T

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

(-) PROSITE Motifs  (3, 3)

Theoretical Model (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.KLK3_HUMAN25-258  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.KLK3_HUMAN61-66  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.KLK3_HUMAN207-218  1A:189-200

(-) Exons   (4, 4)

Theoretical Model (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003260031ENSE00001123926chr19:51358171-5135825787KLK3_HUMAN1-16160--
1.2aENST000003260032aENSE00001718125chr19:51359496-51359655160KLK3_HUMAN16-69541A:16-61 (gaps)46
1.3bENST000003260033bENSE00001268279chr19:51361285-51361571287KLK3_HUMAN69-165971A:61-149 (gaps)101
1.4ENST000003260034ENSE00001268316chr19:51361715-51361851137KLK3_HUMAN165-210461A:149-19246
1.5bENST000003260035bENSE00001268296chr19:51363228-51364020793KLK3_HUMAN211-261511A:193-246 (gaps)55

(-) Sequences/Alignments

Theoretical Model
   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:237
 aligned with KLK3_HUMAN | P07288 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:237
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       
          KLK3_HUMAN     25 IVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPALGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANP  261
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee..eeeeeeeeee..eeee.hhh.....eeee............eeeeeeeeee........................eeeee........................eeeeee...............eeeeeeee.hhhhhhh........eeeee...............eeee..eeeeeeee...........eeeeehhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------K---------------------------------------------------------------------------------------------------I----------------------------------------------T---------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 25-258                                                                                                                                                                                                --- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI--------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2a  PDB: A:16-61 (gaps) UniProt: 16-69-----------------------------------------------------------------------------------------------Exon 1.4  PDB: A:149-192 UniProt: 165-210     Exon 1.5b  PDB: A:193-246 (gaps) UniProt: 211-261   Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3b  PDB: A:61-149 (gaps) UniProt: 69-165                                                  ------------------------------------------------------------------------------------------------ Transcript 1 (2)
                2psa A   16 IVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPALGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANP  246
                                    25        35||      46        56        66||      77        87       95B||||||||96       106       116       127  ||   138      148A       158       168       178     | 187|      196      |210       220 |     229       239       
                                               36|                           67|                        95A||||||95J|                           125|  ||           146||                                184A 188A             203|          221A                         
                                                38                            69                         95B||||||95K                            127  ||            148|                                                       208                                       
                                                                                                          95C||||||                                 130|            148A                                                                                                 
                                                                                                           95D|||||                                  132                                                                                                                 
                                                                                                            95E||||                                                                                                                                                      
                                                                                                             95F|||                                                                                                                                                      
                                                                                                              95G||                                                                                                                                                      
                                                                                                               95H|                                                                                                                                                      
                                                                                                                95I                                                                                                                                                      

Chain I from PDB  Type:PROTEIN  Length:8
                                         
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                2psa I   26 xSSYYSGx   33
                            |      |
                           26-ACE 33-NH2

   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  (0, 0)

(no "SCOP Domain" information available for 2PSA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PSA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Theoretical Model(hide GO term definitions)
Chain A   (KLK3_HUMAN | P07288)
molecular function
    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:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
    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:0002778    antibacterial peptide production    The synthesis or release of an antibacterial peptide during an immune response, resulting in an increase in intracellular or extracellular levels.
    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:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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: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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KLK3_HUMAN | P072881pfa 2zch 2zck 2zcl 3qum

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PSA)