1WQ8A

Crystal structure of vammin, a vegf-f from a snake venom
Total Genus 17
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The genus trace: a function that shows values of genus (vertical axis) for subchains spanned between the first residue, and all other residues (shown on horizontal axis). The number of the latter residue and the genus of a given subchain are shown interactively.

Total Genus
17
sequence length
100
structure length
100
Chain Sequence
EVRPFLEVHERSACQARETLVPILQEYPDEISDIFRPSCVAVLRCSGCCTDESLKCTPVGKHTVDIQIMRVNPRTQSSKMEVMKFTEHTACECRPRRKQG
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The genus matrix. At position (x,y) a genus value for a subchain spanned between x’th and y’th residue is shown. Values of the genus are represented by color, according to the scale given on the right.

Structure visualization

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule tags Toxin
molecule keywords Vascular endothelial growth factor toxin
publication title 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.
pubmed doi rcsb
total genus 17
structure length 100
sequence length 100
ec nomenclature
pdb deposition date 2004-09-23

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00341 PDGF PDGF/VEGF domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.10.90.10 Mainly Beta Ribbon Cystine Knot Cytokines, subunit B Cystine-knot cytokines 1wq8A00
1HRPA 3EVSB 1MKKA 5HI3A 5HK5A 5BPUA 1HCNB 5JZ7A 1TFGA 2GYRA 1FL7A 4KXZA 1WQ9A 1RV6V 4EC7A 3QB4A 1SGFB 4QHUC 4MPLA 2GOOA 4EAXA 4EDXV 2X1WA 1DZ7A 1WQ8A 1LXIA 1QTYR 1REUA 2QCWA 4AY9A 5BQ8A 4YCGC 3S1KV 1M4UA 5HHVA 1NYSB 5FV2V 2X1XE 1HCNA 3JVFA 1QFWB 2VWEA 1BMPA 4HSAA 5FV1V 2KD3A 1M4UL 1SG1A 3BUKA 5BQCA 1TZHV 3V6BA 1JPYA 5BQBA 1TGKA 5F3BC 2GYZA 3P9WA 4X1JA 4YCIC 4EFVA 4XPJA 1B8KA 2P6AA 3IJ2A 1QFWA 5HK5E 1TGJA 1WAQA 4UHYA 4HQXA 2R53A 2XACA 1HCFA 1MJVA 3S1BV 1FZVA 5AEJA 2C7WA 1NYUB 4UI1A 5HHCA 2VPFA 4GLSE 3FUBB 3MJKA 3SEKB 3V2AA 1AGQA 1LX5A 3BDYV 1VPPV 1ES7A 3BMPA 3HH2A 4QCIC 4UHZA 4MIDA 2XV7A 5E4GA 2QCQA 2GNNA 1WWWV 4UI0A 3RJRA 2QR0C 4WPBA 1PDGA 5BQEB 2ASKA 1KLCA 1KTZA 2TGIA 1AOCA 1CZ8V 2QJBA 4HQUA 4EDWV 5F3HI 4LXSJ 1BNDB 3B4VA 4HR9A 1NT3A 1REWA 4UI2B 2B0UA 4FAOA 1B98A 4ZFFC 2FJGV 2PJYA 4LXRJ 1XWDB 5HHXA 5HI5A 3KFDA 3QTKA 2BHKA 4KV5A 5BQEA 4N1DA 2FJHV 4ZBNA 4MQWB 3BK3A 4BV4L 2IFGE 2ARVA 2H62A 2VXSA 1BETA 1B8MB 1BNDA 2QJ9A 1FLTV 1VPFA 2H64A 5HHDA 4KZNA 1HRPB 4GLNE 3EO1C 1MKGA 5BQ8D 1XWDA 3E07A 2QJAA 2V5EB 1KLAA 1BTGA 2GH0C 1FL7B 2ARPA 3MJGA 1TZIV 4QAFC 1E9JA 1HD4A 1WQ9B 2R52A 4MQWA 1KATW 1S4YB 1B8MA 1ZKZA 5HI4A 4AY9B 1BJ1V 5BQ8B
chains in the Genus database with same CATH superfamily
1HRPA 3EVSB 1MKKA 5HI3A 5HK5A 5BPUA 1HCNB 5JZ7A 1TFGA 2GYRA 1FL7A 4KXZA 1WQ9A 1RV6V 4EC7A 3QB4A 1SGFB 4QHUC 4MPLA 2GOOA 4EAXA 4EDXV 2X1WA 1DZ7A 1WQ8A 1LXIA 1QTYR 1REUA 2QCWA 4AY9A 5BQ8A 4YCGC 3S1KV 1M4UA 5HHVA 1NYSB 5FV2V 2X1XE 1HCNA 3JVFA 1QFWB 2VWEA 1BMPA 4HSAA 5FV1V 2KD3A 1M4UL 1SG1A 3BUKA 5BQCA 1TZHV 3V6BA 1JPYA 5BQBA 1TGKA 5F3BC 2GYZA 3P9WA 4X1JA 4YCIC 4EFVA 4XPJA 1B8KA 2P6AA 3IJ2A 1QFWA 5HK5E 1TGJA 1WAQA 4UHYA 4HQXA 2R53A 2XACA 1HCFA 1MJVA 3S1BV 1FZVA 5AEJA 2C7WA 1NYUB 4UI1A 5HHCA 2VPFA 4GLSE 3FUBB 3MJKA 3SEKB 3V2AA 1AGQA 1LX5A 3BDYV 1VPPV 1ES7A 3BMPA 3HH2A 4QCIC 4UHZA 4MIDA 2XV7A 5E4GA 2QCQA 2GNNA 1WWWV 4UI0A 3RJRA 2QR0C 4WPBA 1PDGA 5BQEB 2ASKA 1KLCA 1KTZA 2TGIA 1AOCA 1CZ8V 2QJBA 4HQUA 4EDWV 5F3HI 4LXSJ 1BNDB 3B4VA 4HR9A 1NT3A 1REWA 4UI2B 2B0UA 4FAOA 1B98A 4ZFFC 2FJGV 2PJYA 4LXRJ 1XWDB 5HHXA 5HI5A 3KFDA 3QTKA 2BHKA 4KV5A 5BQEA 4N1DA 2FJHV 4ZBNA 4MQWB 3BK3A 4BV4L 2IFGE 2ARVA 2H62A 2VXSA 1BETA 1B8MB 1BNDA 2QJ9A 1FLTV 1VPFA 2H64A 5HHDA 4KZNA 1HRPB 4GLNE 3EO1C 1MKGA 5BQ8D 1XWDA 3E07A 2QJAA 2V5EB 1KLAA 1BTGA 2GH0C 1FL7B 2ARPA 3MJGA 1TZIV 4QAFC 1E9JA 1HD4A 1WQ9B 2R52A 4MQWA 1KATW 1S4YB 1B8MA 1ZKZA 5HI4A 4AY9B 1BJ1V 5BQ8B
chains in the Genus database with same CATH topology
1HRPA 3EVSB 1MKKA 5HI3A 5HK5A 5BPUA 1HCNB 5JZ7A 1TFGA 2GYRA 1FL7A 4KXZA 1WQ9A 1RV6V 4EC7A 3QB4A 1SGFB 4QHUC 4MPLA 2GOOA 4EAXA 4EDXV 2X1WA 1DZ7A 1WQ8A 1LXIA 1QTYR 1REUA 2QCWA 4AY9A 5BQ8A 4YCGC 3S1KV 1M4UA 5HHVA 1NYSB 5FV2V 2X1XE 1HCNA 3JVFA 1QFWB 2VWEA 1BMPA 4HSAA 5FV1V 2KD3A 1M4UL 1SG1A 3BUKA 5BQCA 1TZHV 3V6BA 1JPYA 5BQBA 1TGKA 5F3BC 2GYZA 3P9WA 4X1JA 4YCIC 4EFVA 4XPJA 1B8KA 2P6AA 3IJ2A 1QFWA 5HK5E 1TGJA 1WAQA 4UHYA 4HQXA 2R53A 2XACA 1HCFA 1MJVA 3S1BV 1FZVA 5AEJA 2C7WA 1NYUB 4UI1A 5HHCA 2VPFA 4GLSE 3FUBB 3MJKA 3SEKB 3V2AA 1AGQA 1LX5A 3BDYV 1VPPV 1ES7A 3BMPA 3HH2A 4QCIC 4UHZA 4MIDA 2XV7A 5E4GA 2QCQA 2GNNA 1WWWV 4UI0A 3RJRA 2QR0C 4WPBA 1PDGA 5BQEB 2ASKA 1KLCA 1KTZA 2TGIA 1AOCA 1CZ8V 2QJBA 4HQUA 4EDWV 5F3HI 4LXSJ 1BNDB 3B4VA 4HR9A 1NT3A 1REWA 4UI2B 2B0UA 4FAOA 1B98A 4ZFFC 2FJGV 2PJYA 4LXRJ 1XWDB 5HHXA 5HI5A 3KFDA 3QTKA 2BHKA 4KV5A 5BQEA 4N1DA 2FJHV 4ZBNA 4MQWB 3BK3A 4BV4L 2IFGE 2ARVA 2H62A 2VXSA 1BETA 1B8MB 1BNDA 2QJ9A 1FLTV 1VPFA 2H64A 5HHDA 4KZNA 1HRPB 4GLNE 3EO1C 1MKGA 5BQ8D 1XWDA 3E07A 2QJAA 2V5EB 1KLAA 1BTGA 2GH0C 1FL7B 2ARPA 3MJGA 1TZIV 4QAFC 1E9JA 1HD4A 1WQ9B 2R52A 4MQWA 1KATW 1S4YB 1B8MA 1ZKZA 5HI4A 4AY9B 1BJ1V 5BQ8B
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1HRP A;  3EVS B;  1MKK A;  5HI3 A;  5HK5 A;  5BPU A;  1HCN B;  5JZ7 A;  1TFG A;  2GYR A;  1FL7 A;  4KXZ A;  1WQ9 A;  1RV6 V;  4EC7 A;  3QB4 A;  1SGF B;  4QHU C;  4MPL A;  2GOO A;  4EAX A;  4EDX V;  2X1W A;  1DZ7 A;  1WQ8 A;  1LXI A;  1QTY R;  1REU A;  2QCW A;  4AY9 A;  5BQ8 A;  4YCG C;  3S1K V;  1M4U A;  5HHV A;  1NYS B;  5FV2 V;  2X1X E;  1HCN A;  3JVF A;  1QFW B;  2VWE A;  1BMP A;  4HSA A;  5FV1 V;  2KD3 A;  1M4U L;  1SG1 A;  3BUK A;  5BQC A;  1TZH V;  3V6B A;  1JPY A;  5BQB A;  1TGK A;  5F3B C;  2GYZ A;  3P9W A;  4X1J A;  4YCI C;  4EFV A;  4XPJ A;  1B8K A;  2P6A A;  3IJ2 A;  1QFW A;  5HK5 E;  1TGJ A;  1WAQ A;  4UHY A;  4HQX A;  2R53 A;  2XAC A;  1HCF A;  1MJV A;  3S1B V;  1FZV A;  5AEJ A;  2C7W A;  1NYU B;  4UI1 A;  5HHC A;  2VPF A;  4GLS E;  3FUB B;  3MJK A;  3SEK B;  3V2A A;  1AGQ A;  1LX5 A;  3BDY V;  1VPP V;  1ES7 A;  3BMP A;  3HH2 A;  4QCI C;  4UHZ A;  4MID A;  2XV7 A;  5E4G A;  2QCQ A;  2GNN A;  1WWW V;  4UI0 A;  3RJR A;  2QR0 C;  4WPB A;  1PDG A;  5BQE B;  2ASK A;  1KLC A;  1KTZ A;  2TGI A;  1AOC A;  1CZ8 V;  2QJB A;  4HQU A;  4EDW V;  5F3H I;  4LXS J;  1BND B;  3B4V A;  4HR9 A;  1NT3 A;  1REW A;  4UI2 B;  2B0U A;  4FAO A;  1B98 A;  4ZFF C;  2FJG V;  2PJY A;  4LXR J;  1XWD B;  5HHX A;  5HI5 A;  3KFD A;  3QTK A;  2BHK A;  4KV5 A;  5BQE A;  4N1D A;  2FJH V;  4ZBN A;  4MQW B;  3BK3 A;  4BV4 L;  2IFG E;  2ARV A;  2H62 A;  2VXS A;  1BET A;  1B8M B;  1BND A;  2QJ9 A;  1FLT V;  1VPF A;  2H64 A;  5HHD A;  4KZN A;  1HRP B;  4GLN E;  3EO1 C;  1MKG A;  5BQ8 D;  1XWD A;  3E07 A;  2QJA A;  2V5E B;  1KLA A;  1BTG A;  2GH0 C;  1FL7 B;  2ARP A;  3MJG A;  1TZI V;  4QAF C;  1E9J A;  1HD4 A;  1WQ9 B;  2R52 A;  4MQW A;  1KAT W;  1S4Y B;  1B8M A;  1ZKZ A;  5HI4 A;  4AY9 B;  1BJ1 V;  5BQ8 B; 
#chains in the Genus database with same CATH topology
 1HRP A;  3EVS B;  1MKK A;  5HI3 A;  5HK5 A;  5BPU A;  1HCN B;  5JZ7 A;  1TFG A;  2GYR A;  1FL7 A;  4KXZ A;  1WQ9 A;  1RV6 V;  4EC7 A;  3QB4 A;  1SGF B;  4QHU C;  4MPL A;  2GOO A;  4EAX A;  4EDX V;  2X1W A;  1DZ7 A;  1WQ8 A;  1LXI A;  1QTY R;  1REU A;  2QCW A;  4AY9 A;  5BQ8 A;  4YCG C;  3S1K V;  1M4U A;  5HHV A;  1NYS B;  5FV2 V;  2X1X E;  1HCN A;  3JVF A;  1QFW B;  2VWE A;  1BMP A;  4HSA A;  5FV1 V;  2KD3 A;  1M4U L;  1SG1 A;  3BUK A;  5BQC A;  1TZH V;  3V6B A;  1JPY A;  5BQB A;  1TGK A;  5F3B C;  2GYZ A;  3P9W A;  4X1J A;  4YCI C;  4EFV A;  4XPJ A;  1B8K A;  2P6A A;  3IJ2 A;  1QFW A;  5HK5 E;  1TGJ A;  1WAQ A;  4UHY A;  4HQX A;  2R53 A;  2XAC A;  1HCF A;  1MJV A;  3S1B V;  1FZV A;  5AEJ A;  2C7W A;  1NYU B;  4UI1 A;  5HHC A;  2VPF A;  4GLS E;  3FUB B;  3MJK A;  3SEK B;  3V2A A;  1AGQ A;  1LX5 A;  3BDY V;  1VPP V;  1ES7 A;  3BMP A;  3HH2 A;  4QCI C;  4UHZ A;  4MID A;  2XV7 A;  5E4G A;  2QCQ A;  2GNN A;  1WWW V;  4UI0 A;  3RJR A;  2QR0 C;  4WPB A;  1PDG A;  5BQE B;  2ASK A;  1KLC A;  1KTZ A;  2TGI A;  1AOC A;  1CZ8 V;  2QJB A;  4HQU A;  4EDW V;  5F3H I;  4LXS J;  1BND B;  3B4V A;  4HR9 A;  1NT3 A;  1REW A;  4UI2 B;  2B0U A;  4FAO A;  1B98 A;  4ZFF C;  2FJG V;  2PJY A;  4LXR J;  1XWD B;  5HHX A;  5HI5 A;  3KFD A;  3QTK A;  2BHK A;  4KV5 A;  5BQE A;  4N1D A;  2FJH V;  4ZBN A;  4MQW B;  3BK3 A;  4BV4 L;  2IFG E;  2ARV A;  2H62 A;  2VXS A;  1BET A;  1B8M B;  1BND A;  2QJ9 A;  1FLT V;  1VPF A;  2H64 A;  5HHD A;  4KZN A;  1HRP B;  4GLN E;  3EO1 C;  1MKG A;  5BQ8 D;  1XWD A;  3E07 A;  2QJA A;  2V5E B;  1KLA A;  1BTG A;  2GH0 C;  1FL7 B;  2ARP A;  3MJG A;  1TZI V;  4QAF C;  1E9J A;  1HD4 A;  1WQ9 B;  2R52 A;  4MQW A;  1KAT W;  1S4Y B;  1B8M A;  1ZKZ A;  5HI4 A;  4AY9 B;  1BJ1 V;  5BQ8 B; 
#chains in the Genus database with same CATH homology
 1HRP A;  3EVS B;  1MKK A;  5HI3 A;  5HK5 A;  5BPU A;  1HCN B;  5JZ7 A;  1TFG A;  2GYR A;  1FL7 A;  4KXZ A;  1WQ9 A;  1RV6 V;  4EC7 A;  3QB4 A;  1SGF B;  4QHU C;  4MPL A;  2GOO A;  4EAX A;  4EDX V;  2X1W A;  1DZ7 A;  1WQ8 A;  1LXI A;  1QTY R;  1REU A;  2QCW A;  4AY9 A;  5BQ8 A;  4YCG C;  3S1K V;  1M4U A;  5HHV A;  1NYS B;  5FV2 V;  2X1X E;  1HCN A;  3JVF A;  1QFW B;  2VWE A;  1BMP A;  4HSA A;  5FV1 V;  2KD3 A;  1M4U L;  1SG1 A;  3BUK A;  5BQC A;  1TZH V;  3V6B A;  1JPY A;  5BQB A;  1TGK A;  5F3B C;  2GYZ A;  3P9W A;  4X1J A;  4YCI C;  4EFV A;  4XPJ A;  1B8K A;  2P6A A;  3IJ2 A;  1QFW A;  5HK5 E;  1TGJ A;  1WAQ A;  4UHY A;  4HQX A;  2R53 A;  2XAC A;  1HCF A;  1MJV A;  3S1B V;  1FZV A;  5AEJ A;  2C7W A;  1NYU B;  4UI1 A;  5HHC A;  2VPF A;  4GLS E;  3FUB B;  3MJK A;  3SEK B;  3V2A A;  1AGQ A;  1LX5 A;  3BDY V;  1VPP V;  1ES7 A;  3BMP A;  3HH2 A;  4QCI C;  4UHZ A;  4MID A;  2XV7 A;  5E4G A;  2QCQ A;  2GNN A;  1WWW V;  4UI0 A;  3RJR A;  2QR0 C;  4WPB A;  1PDG A;  5BQE B;  2ASK A;  1KLC A;  1KTZ A;  2TGI A;  1AOC A;  1CZ8 V;  2QJB A;  4HQU A;  4EDW V;  5F3H I;  4LXS J;  1BND B;  3B4V A;  4HR9 A;  1NT3 A;  1REW A;  4UI2 B;  2B0U A;  4FAO A;  1B98 A;  4ZFF C;  2FJG V;  2PJY A;  4LXR J;  1XWD B;  5HHX A;  5HI5 A;  3KFD A;  3QTK A;  2BHK A;  4KV5 A;  5BQE A;  4N1D A;  2FJH V;  4ZBN A;  4MQW B;  3BK3 A;  4BV4 L;  2IFG E;  2ARV A;  2H62 A;  2VXS A;  1BET A;  1B8M B;  1BND A;  2QJ9 A;  1FLT V;  1VPF A;  2H64 A;  5HHD A;  4KZN A;  1HRP B;  4GLN E;  3EO1 C;  1MKG A;  5BQ8 D;  1XWD A;  3E07 A;  2QJA A;  2V5E B;  1KLA A;  1BTG A;  2GH0 C;  1FL7 B;  2ARP A;  3MJG A;  1TZI V;  4QAF C;  1E9J A;  1HD4 A;  1WQ9 B;  2R52 A;  4MQW A;  1KAT W;  1S4Y B;  1B8M A;  1ZKZ A;  5HI4 A;  4AY9 B;  1BJ1 V;  5BQ8 B; 
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similar chains in the Genus database (?% sequence similarity)
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similar chains in the pdb database (?% sequence similarity)

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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