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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DISINTEGRIN, TRIMESTATIN
 
Authors :  Y. Fujii, D. Okuda, Z. Fujimoto, T. Morita, H. Mizuno
Date :  06 Jan 03  (Deposition) - 07 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Disintegrin, Rgd Motif, Trimestatin, Snake Venom, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Fujii, D. Okuda, Z. Fujimoto, T. Horii, T. Morita, H. Mizuno
Crystal Structure Of Trimestatin, A Disintegrin Containing A Cell Adhesion Recognition Motif Rgd
J. Mol. Biol. V. 332 1115 2003
PubMed-ID: 14499613  |  Reference-DOI: 10.1016/S0022-2836(03)00991-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DISINTEGRIN TRIFLAVIN
    Chains: A
    Organism Scientific: TRIMERESURUS FLAVOVIRIDIS
    Organism Taxid: 88087
    Secretion: VENOM
    Synonym: TRIMESTATIN, RGD-CONTAINING PEPTIDE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , SER A:8 , ASN A:11 , HOH A:725 , HOH A:746 , HOH A:844BINDING SITE FOR RESIDUE SO4 A 701

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
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 1J2L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J2L)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DISINTEGRIN_2PS50214 Disintegrin domain profile.VM2T_PROFL1-70  1A:1-68
2DISINTEGRIN_1PS00427 Disintegrins signature.VM2T_PROFL27-46  1A:27-46

(-) Exons   (0, 0)

(no "Exon" information available for 1J2L)

(-) 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:68
 aligned with VM2T_PROFL | P21859 from UniProtKB/Swiss-Prot  Length:70

    Alignment length:68
                                    10        20        30        40        50        60        
            VM2T_PROFL    1 GEECDCGSPSNPCCDAATCKLRPGAQCADGLCCDQCRFKKKRTICRIARGDFPDDRCTGQSADCPRWN 68
               SCOP domains d1j2la_ A: Flavoridin (triflavin)                                    SCOP domains
               CATH domains 1j2lA00 A:1-68 Echistatin                                            CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................ee..ee.....eee........ee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) DISINTEGRIN_2  PDB: A:1-68 UniProt: 1-70                             PROSITE (1)
                PROSITE (2) --------------------------DISINTEGRIN_1       ---------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------- Transcript
                  1j2l A  1 GEECDCGSPSNPCCDAATCKLRPGAQCADGLCCDQCRFKKKRTICRIARGDFPDDRCTGQSADCPRWN 68
                                    10        20        30        40        50        60
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  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: Small proteins (3458)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Few Secondary Structures (1120)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J2L)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VM2T_PROFL | P21859)
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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  1j2l
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