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(-) Description

Title :  SOLUTION STRUCTURE OF RHODOSTOMIN
 
Authors :  W. J. Chuang, Y. C. Chen, C. Y. Chen, Y. T. Chang
Date :  16 Apr 07  (Deposition) - 08 May 07  (Release) - 21 Apr 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Disintegrin, Rhodostomin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Chen, J. H. Shiu, Y. H. Hsieh, Y. C. Liu, Y. C. Chen, Y. C. Chen, W. Y. Jeng, M. J. Tang, S. J. Lo, W. J. Chuang
Effect Of D To E Mutation Of The Rgd Motif In Rhodostomin On Its Activity, Structure, And Dynamics: Importance Of The Interactions Between The D Residue And Integrin
Proteins 2009
PubMed-ID: 19280603  |  Reference-DOI: 10.1002/PROT.22387
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHODOSTOXIN-DISINTEGRIN RHODOSTOMIN
    Chains: A
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPICZAA
    Expression System Strain: X33
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-68
    Gene: RHOD
    Organism Common: MALAYAN PIT VIPER
    Organism Scientific: CALLOSELASMA RHODOSTOMA
    Organism Taxid: 8717

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2PJF)

(-) SS Bonds  (6, 6)

NMR Structure
No.Residues
1A:4 -A:19
2A:6 -A:14
3A:13 -A:36
4A:27 -A:33
5A:32 -A:57
6A:45 -A:64

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DISINTEGRIN_1PS00427 Disintegrins signature.VM2RH_CALRH434-453  1A:27-46

(-) Exons   (0, 0)

(no "Exon" information available for 2PJF)

(-) 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:68
 aligned with VM2RH_CALRH | P30403 from UniProtKB/Swiss-Prot  Length:478

    Alignment length:68
                                   417       427       437       447       457       467        
          VM2RH_CALRH   408 GKECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIPRGDMPDDRCTGQSADCPRYH 475
               SCOP domains d2pjfa_ A: Kistrin (rhodostomin)                                     SCOP domains
               CATH domains 2pjfA00 A:1-68 Echistatin                                            CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee....ee...........ee..ee..eeeeee........eeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------DISINTEGRIN_1       ---------------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 2pjf A   1 GKECDCSSPENPCCDAATCKLRPGAQCGEGLCCEQCKFSRAGKICRIPRGDMPDDRCTGQSADCPRYH  68
                                    10        20        30        40        50        60
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 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 2PJF)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (VM2RH_CALRH | P30403)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

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  3.4.24.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        VM2RH_CALRH | P30403: 1n4y 1q7i 1q7j 2ljv 2m75 2m7f 2m7h 2pjg 2pji 3uci 4m4c 4r5r 4r5u 4rqg

(-) Related Entries Specified in the PDB File

5117