Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  X-RAY ANALYSES OF ASPARTIC PROTEASES. II. THREE-DIMENSIONAL STRUCTURE OF THE HEXAGONAL CRYSTAL FORM OF PORCINE PEPSIN AT 2.3 ANGSTROMS RESOLUTION
 
Authors :  J. B. Cooper, G. Khan, G. Taylor, I. J. Tickle, T. L. Blundell
Date :  30 May 90  (Deposition) - 15 Jul 90  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase(Acid Proteinase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Cooper, G. Khan, G. Taylor, I. J. Tickle, T. L. Blundell
X-Ray Analyses Of Aspartic Proteinases. Ii. Three-Dimensional Structure Of The Hexagonal Crystal Form O Porcine Pepsin At 2. 3 A Resolution.
J. Mol. Biol. V. 214 199 1990
PubMed-ID: 2115088  |  Reference-DOI: 10.1016/0022-2836(90)90156-G

(-) Compounds

Molecule 1 - PEPSIN
    Chains: A
    EC Number: 3.4.23.1
    Engineered: YES
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5PEP)

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1CATUNKNOWNASP A:32 , ASP A:215 , HOH A:328NULL

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:45 -A:50
2A:206 -A:210
3A:250 -A:283

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:22 -Pro A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5PEP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5PEP)

(-) Exons   (0, 0)

(no "Exon" information available for 5PEP)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d5pepa_ A: Pepsin(ogen)                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 5pepA01 A:1-170 Acid Proteases                                                                                                                                            5pepA02 A:171-327 Acid Proteases                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eeeeeeee....eeeeeeee.....eee.......hhh.......hhh....eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeeeeeee...hhhhh....eeee...hhh.hhh...hhhhhhh.......eeeee........eeeee............eeee.......eeee.eeee..eeee....eeeee......eee.hhhhhhhhhhh..ee.....eee...hhhh...eeeee..eeeee.hhhh......eeeeeeeee.........eee.hhhh..eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5pep A   1 IGDEPLENYLDTEYFGTIGIGTPAQDFTVIFDTGSSNLWVPSVYCSSLACSDHNQFNPDDSSTFEATSQELSITYGTGSMTGILGYDTVQVGGISDTNQIFGLSETEPGSFLYYAPFDGILGLAYPSISASGATPVFDNLWDQGLVSQDLFSVYLSSNDDSGSVVLLGGIDSSYYTGSLNWVPVSVEGYWQITLDSITMDGETIACSGGCQAIVDTGTSLLTGPTSAIANIQSDIGASENSDGEMVISCSSIASLPDIVFTINGVQYPLSPSAYILQDDDSCTSGFEGMDVPTSSGELWILGDVFIRQYYTVFDRANNKVGLAPVA 327
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       231       241       251       261       271       281       291       301       311       321      
                                                                                                                                                                                                                                                              229|                                                                                                
                                                                                                                                                                                                                                                               231
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5PEP)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 5pep)
 
  Sites
    CAT  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Thr A:22 - Pro A:23   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5pep
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PEPA_PIG | P00791
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.23.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PEPA_PIG | P00791
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PEPA_PIG | P00791: 1f34 1psa 1yx9 2psg 3pep 3psg 4pep

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5PEP)