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(-) Description

Title :  CRYSTAL STRUCTURE OF VR-1, A VEGF-F FROM A SNAKE VENOM
 
Authors :  K. Suto, Y. Yamazaki, T. Morita, H. Mizuno
Date :  24 Sep 04  (Deposition) - 07 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Snake Venom, Vascular Endothelial Growth Factor, Vegf, Vegf- F, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Suto, Y. Yamazaki, T. Morita, H. Mizuno
Crystal Structures Of Novel Vascular Endothelial Growth Factors (Vegf) From Snake Venoms: Insight Into Selective Vegf Binding To Kinase Insert Domain-Containing Receptor But Not To Fms-Like Tyrosine Kinase-1.
J. Biol. Chem. V. 280 2126 2005
PubMed-ID: 15542594  |  Reference-DOI: 10.1074/JBC.M411395200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VASCULAR ENDOTHELIAL GROWTH FACTOR
    Chains: A
    Organism Scientific: DABOIA RUSSELLII RUSSELLII
    Organism Taxid: 31159
    Secretion: VENOM
    Strain: RUSSELLII
    Synonym: VR-1, VEGF-F
 
Molecule 2 - VASCULAR ENDOTHELIAL GROWTH FACTOR
    Chains: B
    Organism Scientific: DABOIA RUSSELLII RUSSELLII
    Organism Taxid: 31159
    Secretion: VENOM
    Strain: RUSSELLII
    Synonym: VR-1, VEGF-F

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 1WQ9)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:14 -A:56
2A:39 -B:48
3A:45 -A:91
4A:48 -B:39
5A:49 -A:93
6B:14 -B:56
7B:45 -B:91
8B:49 -B:93

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:36 -Pro A:37
2Arg B:36 -Pro B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WQ9)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDGF_2PS50278 Platelet-derived growth factor (PDGF) family profile.TXVE_DABRR25-122
 		  2A:2-95
B:2-95
2PDGF_1PS00249 Platelet-derived growth factor (PDGF) family signature.TXVE_DABRR61-73
 		  2A:37-49
B:37-49

(-) Exons   (0, 0)

(no "Exon" information available for 1WQ9)

(-) 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:96
 aligned with TXVE_DABRR | P67861 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:96
                                    34        44        54        64        74        84        94       104       114      
           TXVE_DABRR    25 QVRPFLDVYERSACQTRETLVSILQEHPDEISDIFRPSCVAVLRCSGCCTDESMKCTPVGKHTADIQIMRMNPRTHSSKMEVMKFMEHTACECRPR 120
               SCOP domains d1wq9a_ A: Vascular endothelial growth factor, VEGF                                              SCOP domains
               CATH domains 1wq9A00 A:1-96 Cystine-knot cytokines                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee.......eeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PDGF_2  PDB: A:2-95 UniProt: 25-122                                                              PROSITE (1)
                PROSITE (2) ------------------------------------PDGF_1       ----------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1wq9 A   1 EVRPFLDVYQRSACQTRETLVSILQEHPDEISDIFRPSCVAVLRCSGCCTDESMKCTPVGKHTADIQIMRMNPRTHSSKMEVMKFMEHTACECRPA  96
                                    10        20        30        40        50        60        70        80        90      


Chain B from PDB  Type:PROTEIN  Length:96
 aligned with TXVE_DABRR | P67861 from UniProtKB/Swiss-Prot  Length:144

    Alignment length:96
                                    34        44        54        64        74        84        94       104       114      
           TXVE_DABRR    25 QVRPFLDVYERSACQTRETLVSILQEHPDEISDIFRPSCVAVLRCSGCCTDESMKCTPVGKHTADIQIMRMNPRTHSSKMEVMKFMEHTACECRPR 120
               SCOP domains d1wq9b_ B: Vascular endothelial growth factor, VEGF                                              SCOP domains
               CATH domains -1wq9B00 B:2-96 Cystine-knot cytokines                                                           CATH domains
           Pfam domains (1) -------------PDGF-1wq9B01 B:14-71                                      ------------------------- Pfam domains (1)
           Pfam domains (2) -------------PDGF-1wq9B02 B:14-71                                      ------------------------- Pfam domains (2)
         Sec.struct. author .eehhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee........eeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PDGF_2  PDB: B:2-95 UniProt: 25-122                                                              PROSITE (1)
                PROSITE (2) ------------------------------------PDGF_1       ----------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 1wq9 B   1 xVRPFLDVYQRSACQTRETLVSILQEHPDEISDIFRPSCVAVLRCSGCCTDESMKCTPVGKHTADIQIMRMNPRTHSSKMEVMKFMEHTACECRPA  96
                            |       10        20        30        40        50        60        70        80        90      
                            1-PCA
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Cystine-knot (56)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TXVE_DABRR | P67861)
molecular function
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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(-) Related Entries Specified in the PDB File

1wq8 VAMMIN, A VEGF-F FROM A SNAKE VENOM