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(-) Description

Title :  CRYSTAL STRUCTURE OF VAMMIN, A VEGF-F FROM A SNAKE VENOM
 
Authors :  K. Suto, Y. Yamazaki, T. Morita, H. Mizuno
Date :  23 Sep 04  (Deposition) - 07 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (8x)
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 Bu 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 TOXIN
    Chains: A
    Organism Scientific: VIPERA ASPIS ASPIS
    Organism Taxid: 194601
    Secretion: VENOM
    Strain: ASPIS
    Synonym: VR-1, VEGF-F

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (8x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1PCA2Mod. Amino AcidPYROGLUTAMIC ACID
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
1PCA8Mod. Amino AcidPYROGLUTAMIC ACID
2TRS8Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:20 , PRO A:22 , GLY A:47 , CYS A:48 , HOH A:1008 , HOH A:1045 , HOH A:1071 , HOH A:1081 , HOH A:1118BINDING SITE FOR RESIDUE TRS A 1173

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:14 -A:56
2A:39 -A:48
3A:45 -A:91
4A:49 -A:93

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:36 -Pro A:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TXVE_VIPAP_001 *H62WTXVE_VIPAP  ---  ---AH62W
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TXVE_VIPAP_001 *H62WTXVE_VIPAP  ---  ---AH62W
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_TXVE_VIPAP_001 *H62WTXVE_VIPAP  ---  ---AH62W
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDGF_2PS50278 Platelet-derived growth factor (PDGF) family profile.TXVE_VIPAP1-98  1A:2-98
TXVE_VIPAA25-122  1A:2-98
2PDGF_1PS00249 Platelet-derived growth factor (PDGF) family signature.TXVE_VIPAP37-49  1A:37-49
TXVE_VIPAA61-73  1A:37-49
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDGF_2PS50278 Platelet-derived growth factor (PDGF) family profile.TXVE_VIPAP1-98  2A:2-98
TXVE_VIPAA25-122  2A:2-98
2PDGF_1PS00249 Platelet-derived growth factor (PDGF) family signature.TXVE_VIPAP37-49  2A:37-49
TXVE_VIPAA61-73  2A:37-49
Biological Unit 2 (2, 32)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDGF_2PS50278 Platelet-derived growth factor (PDGF) family profile.TXVE_VIPAP1-98  8A:2-98
TXVE_VIPAA25-122  8A:2-98
2PDGF_1PS00249 Platelet-derived growth factor (PDGF) family signature.TXVE_VIPAP37-49  8A:37-49
TXVE_VIPAA61-73  8A:37-49

(-) Exons   (0, 0)

(no "Exon" information available for 1WQ8)

(-) 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:100
 aligned with TXVE_VIPAA | P67863 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:100
                                    34        44        54        64        74        84        94       104       114       124
           TXVE_VIPAA    25 QVRPFLEVHERSACQARETLVPILQEYPDEISDIFRPSCVAVLRCSGCCTDESLKCTPVGKHTVDLQIMRVNPRTQSSKMEVMKFTEHTACECRPRRKQG 124
               SCOP domains d1wq8a_ A: Vascular endothelial growth factor, VEGF                                                  SCOP domains
               CATH domains -1wq8A00 A:2-100 Cystine-knot cytokines                                                              CATH domains
               Pfam domains -------------PDGF-1wq8A01 A:14-86                                                     -------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee........eeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------W-------------------------------------- SAPs(SNPs)
                PROSITE (2) PDGF_2  PDB: A:2-98 UniProt: 25-122                                                               -- PROSITE (2)
                PROSITE (3) ------------------------------------PDGF_1       --------------------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1wq8 A   1 xVRPFLEVHERSACQARETLVPILQEYPDEISDIFRPSCVAVLRCSGCCTDESLKCTPVGKHTVDIQIMRVNPRTQSSKMEVMKFTEHTACECRPRRKQG 100
                            |       10        20        30        40        50        60        70        80        90       100
                            |                                                                                                   
                            1-PCA                                                                                               


Chain A from PDB  Type:PROTEIN  Length:100
 aligned with TXVE_VIPAP | P83942 from UniProtKB/Swiss-Prot  Length:110

    Alignment length:100
                                    10        20        30        40        50        60        70        80        90       100
           TXVE_VIPAP     1 QVRPFLEVHERSACQARETLVSILQEYPDEISDIFRPSCVAVLRCSGCCTDESLKCTPVGKHTVDLQIMRVNPRTQSSKMEVMKFTEHTACECRPRRKQG 100
               SCOP domains d1wq8a_ A: Vascular endothelial growth factor, VEGF                                                  SCOP domains
               CATH domains -1wq8A00 A:2-100 Cystine-knot cytokines                                                              CATH domains
               Pfam domains -------------PDGF-1wq8A01 A:14-86                                                     -------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.eeeeeeeehhhhh......eee..eeeeeeee........eeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------W-------------------------------------- SAPs(SNPs)
                PROSITE (1) PDGF_2  PDB: A:2-98 UniProt: 1-98                                                                 -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ------------------------------------PDGF_1       --------------------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 1wq8 A   1 xVRPFLEVHERSACQARETLVPILQEYPDEISDIFRPSCVAVLRCSGCCTDESLKCTPVGKHTVDIQIMRVNPRTQSSKMEVMKFTEHTACECRPRRKQG 100
                            |       10        20        30        40        50        60        70        80        90       100
                            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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (3, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (TXVE_VIPAP | P83942)
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.

Chain A   (TXVE_VIPAA | P67863)
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

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(-) Related Entries Specified in the PDB File

1wq9 VR-1, A VEGF-F FROM A SNAKE VENOM