Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CARICA PAPAYA CHYMOPAPAIN AT 1.7 ANGSTROMS RESOLUTION
 
Authors :  D. Maes, J. Bouckaert, F. Poortmans, L. Wyns, Y. Looze
Date :  20 Jun 96  (Deposition) - 23 Dec 96  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase, Thiol Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Maes, J. Bouckaert, F. Poortmans, L. Wyns, Y. Looze
Structure Of Chymopapain At 1. 7 A Resolution.
Biochemistry V. 35 16292 1996
PubMed-ID: 8973203  |  Reference-DOI: 10.1021/BI961491W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHYMOPAPAIN
    Chains: A
    EC Number: 3.4.22.6
    Organ: FRUIT
    Organism Common: PAPAYA
    Organism Scientific: CARICA PAPAYA
    Organism Taxid: 3649
    Other Details: THE ACTIVE SITE CYS 25 AS WELL AS CYS 117 ARE PROTECTED WITH A THIOMETHYL GROUP

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SCH2Mod. Amino AcidS-METHYL-THIO-CYSTEINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SCH4Mod. Amino AcidS-METHYL-THIO-CYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 1YAL)

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:22 -A:63
2A:56 -A:95
3A:153 -A:204

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:151 -Pro A:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YAL)

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.PAPA2_CARPA153-164  1A:19-30
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.PAPA2_CARPA291-301  1A:157-167
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.PAPA2_CARPA308-327  1A:174-193
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.PAPA2_CARPA153-164  2A:19-30
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.PAPA2_CARPA291-301  2A:157-167
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.PAPA2_CARPA308-327  2A:174-193

(-) Exons   (0, 0)

(no "Exon" information available for 1YAL)

(-) Sequences/Alignments

Asymmetric 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:218
 aligned with PAPA2_CARPA | P14080 from UniProtKB/Swiss-Prot  Length:352

    Alignment length:218
                                   144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344        
          PAPA2_CARPA   135 YPQSIDWRAKGAVTPVKNQGACGSCWAFSTIATVEGINKIVTGNLLELSEQELVDCDKHSYGCKGGYQTTSLQYVANNGVHTSKVYPYQAKQYKCRATDKPGPKVKITGYKRVPSNCETSFLGALANQPLSVLVEAGGKPFQLYKSGVFDGPCGTKLDHAVTAVGYGTSDGKNYIIIKNSWGPNWGEKGYMRLKRQSGNSQGTCGVYKSSYYPFKGFA 352
               SCOP domains d1yala_ A: Chymopapain                                                                                                                                                                                                     SCOP domains
               CATH domains 1yalA00 A:1-218 Cysteine proteinases                                                                                                                                                                                       CATH domains
               Pfam domains Peptidase_C1-1yalA01 A:1-214                                                                                                                                                                                          ---- Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhhhh.......hhhhhhh.....hhh...hhhhhhhhhhh..................hhh.........eeee.....hhhhhhhh....eeeee....hhhh................eeeeeeeeeee..eeeeeee...........eeeee........hhh.....eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yal A   1 YPQSIDWRAKGAVTPVKNQGACGScWAFSTIATVEGINKIVTGNLLELSEQELVDCDKHSYGCKGGYQTTSLQYVANNGVHTSKVYPYQAKQYKCRATDKPGPKVKITGYKRVPSNcETSFLGALANQPLSVLVEAGGKPFQLYKSGVFDGPCGTKLDHAVTAVGYGTSDGKNYIIIKNSWGPNWGEKGYMRLKRQSGNSQGTCGVYKSSYYPFKGFA 218
                                    10        20    |   30        40        50        60        70        80        90       100       110      |120       130       140       150       160       170       180       190       200       210        
                                                   25-SCH                                                                                     117-SCH
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Peptidase_CA (169)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (PAPA2_CARPA | P14080)
molecular function
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

 Visualization

(-) Interactive Views

Asymmetric 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
    SCH  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1yal)
 
  Cis Peptide Bonds
    Gly A:151 - Pro A:152   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  1yal
    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
  PAPA2_CARPA | P14080
    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)
  3.4.22.6
    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
  PAPA2_CARPA | P14080
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1YAL)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YAL)