Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF JERDOSTATIN FROM TRIMERESURUS JERDONII
 
Authors :  R. J. Carbajo, L. Sanz, S. Mosulen, J. J. Calvete, A. Pineda-Lucena
Date :  27 Jan 09  (Deposition) - 31 Mar 10  (Release) - 09 Nov 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (40x)
NMR Structure *:  A  (1x)
Keywords :  Venom, Toxin, Cell Adhesion, Blood Coagulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Carbajo, L. Sanz, S. Mosulen, A. Perez, C. Marcinkiewicz, A. Pineda-Lucena, J. J. Calvete
Nmr Structure And Dynamics Of Recombinant Wild-Type And Mutated Jerdostatin, A Selective Inhibitor Of Integrin Alpha1 Beta1
Proteins V. 79 2530 2011
PubMed-ID: 21656569  |  Reference-DOI: 10.1002/PROT.23076

(-) Compounds

Molecule 1 - SHORT DISINTEGRIN JERDOSTATIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-32A
    Fragment: RESIDUES 68-110
    Organism Common: JERDON'S PIT-VIPER
    Organism Scientific: TRIMERESURUS JERDONII
    Organism Taxid: 135726
    Synonym: JERDOSTATIN

 Structural Features

(-) Chains, Units

  1
NMR Structure (40x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2W9O)

(-) Sites  (0, 0)

(no "Site" information available for 2W9O)

(-) SS Bonds  (4, 4)

NMR Structure
No.Residues
1A:4 -A:13
2A:9 -A:32
3A:10 -A:37
4A:22 -A:39

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W9O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W9O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W9O)

(-) Exons   (0, 0)

(no "Exon" information available for 2W9O)

(-) Sequences/Alignments

NMR Structure
   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:46
 aligned with DIS_PROJR | Q7ZZM2 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:55
                                    65        75        85        95       105     
            DIS_PROJR    56 PMKGNTLQKLPLCTTGPCCRQCKLKPAGTTCWRTSVSSHYCTGRSCECPSYPGNG 110
               SCOP domains d2w         9oa_ A: automated matches                   SCOP domains
               CATH domains 2w9         oA00 A:1-46 Echistatin                      CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author ...---------........................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                 2w9o A   1 AMD---------CTTGPCCRQCKLKPAGTTCWRTSVSSHYCTGRSCECPSYPGNG  46
                              |      -  |     11        21        31        41     
                              3         4
   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)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W9O)

(-) Gene Ontology  (1, 1)

NMR Structure(hide GO term definitions)
Chain A   (DIS_PROJR | Q7ZZM2)
cellular component
    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.

 Visualization

(-) Interactive Views

NMR Structure
  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 2w9o)
 
  Sites
(no "Sites" information available for 2w9o)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2w9o)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2w9o
    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
  DIS_PROJR | Q7ZZM2
    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)
  (no 'Enzyme Classificator' available)
    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
  DIS_PROJR | Q7ZZM2
    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
        DIS_PROJR | Q7ZZM2: 2w9u 2w9v 2w9w

(-) Related Entries Specified in the PDB File

2w9u SOLUTION STRUCTURE OF JERDOSTATIN MUTANT R24K FROM TRIMERESURUS JERDONII
2w9v SOLUTION STRUCTURE OF JERDOSTATIN FROM TRIMERESURUS JERDONII WITH END C-TERMINAL RESIDUES N45G46 DELETED
2w9w SOLUTION STRUCTURE OF JERDOSTATIN MUTANT R24K FROM TRIMERESURUS JERDONII WITH END C- TERMINAL RESIDUES N45G46 DELETED