4HQUA

Crystal structure of human pdgf-bb in complex with a modified nucleotide aptamer (somamer sl5)
Total Genus 12
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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
12
sequence length
95
structure length
95
Chain Sequence
IAEPAMIAECKTRTEVFEISRRLIDRTNANFLVWPPCVEVQRCSGCCNNRNVQCRPTQVQLRPVQVRKIEIVRKKPIFKKATVTLEDHLACKCET
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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 Hormone/dna
molecule keywords Platelet-derived growth factor subunit B
publication title Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets.
pubmed doi rcsb
source organism Homo sapiens
total genus 12
structure length 95
sequence length 95
ec nomenclature
pdb deposition date 2012-10-26

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 4hquA00
3JVFA 3P9WA 3IJ2A 4KZNA 4LXRJ 1FLTV 4EFVA 4N1DA 4YCIC 5BQ8D 1LX5A 1AOCA 1ZKZA 1BJ1V 2B0UA 3HH2A 2PJYA 1ES7A 1B8KA 2VXSA 2GH0C 2FJHV 1WQ9B 2P6AA 2QCQA 4FAOA 4QHUC 4MQWB 2X1XE 4QCIC 5BQEB 1NT3A 4AY9A 5BQ8A 1M4UL 5HK5E 1PDGA 1WQ8A 2QJAA 1M4UA 3EO1C 4UI2B 5BQCA 3BK3A 1HRPB 2ARPA 3BUKA 5HHXA 4WPBA 5F3HI 2BHKA 2R52A 4MIDA 2X1WA 2VPFA 4EDXV 1BETA 5FV1V 1REWA 4QAFC 1TZHV 5BQBA 2GOOA 3B4VA 4UHYA 1XWDB 1BNDB 1HCFA 3MJGA 1LXIA 1RV6V 1WQ9A 5HK5A 5HHCA 4HQUA 4MQWA 1NYUB 2FJGV 5BQEA 1QFWB 1KATW 1VPPV 1S4YB 1SGFB 1WAQA 3FUBB 4BV4L 1VPFA 3S1KV 1HCNB 3KFDA 1B98A 5HHDA 3QTKA 1HRPA 3E07A 1NYSB 4YCGC 5HI4A 2H64A 4MPLA 5HI3A 2QJBA 2QJ9A 4HR9A 2ASKA 2V5EB 3SEKB 5HI5A 1E9JA 2GYZA 1B8MB 1XWDA 1MKKA 4EDWV 1HD4A 5JZ7A 4AY9B 1BNDA 4UI0A 1REUA 2H62A 5BPUA 1MJVA 2GYRA 1BMPA 2C7WA 3QB4A 1FL7B 1QFWA 4HSAA 3V6BA 5FV2V 1KLCA 1KLAA 2GNNA 2IFGE 2XV7A 4ZFFC 3BDYV 2XACA 4KXZA 5AEJA 1WWWV 1QTYR 2ARVA 1HCNA 1JPYA 2R53A 2QCWA 4LXSJ 4XPJA 4ZBNA 2KD3A 3S1BV 5E4GA 4GLSE 3BMPA 1TZIV 1CZ8V 4KV5A 2QR0C 3RJRA 1TGKA 1TGJA 4GLNE 4X1JA 4HQXA 2TGIA 4EAXA 1KTZA 1B8MA 4UI1A 5BQ8B 4UHZA 1TFGA 1SG1A 1DZ7A 4EC7A 1AGQA 5F3BC 5HHVA 1BTGA 3V2AA 1MKGA 2VWEA 3EVSB 1FL7A 3MJKA 1FZVA
chains in the Genus database with same CATH superfamily
3JVFA 3P9WA 3IJ2A 4KZNA 4LXRJ 1FLTV 4EFVA 4N1DA 4YCIC 5BQ8D 1LX5A 1AOCA 1ZKZA 1BJ1V 2B0UA 3HH2A 2PJYA 1ES7A 1B8KA 2VXSA 2GH0C 2FJHV 1WQ9B 2P6AA 2QCQA 4FAOA 4QHUC 4MQWB 2X1XE 4QCIC 5BQEB 1NT3A 4AY9A 5BQ8A 1M4UL 5HK5E 1PDGA 1WQ8A 2QJAA 1M4UA 3EO1C 4UI2B 5BQCA 3BK3A 1HRPB 2ARPA 3BUKA 5HHXA 4WPBA 5F3HI 2BHKA 2R52A 4MIDA 2X1WA 2VPFA 4EDXV 1BETA 5FV1V 1REWA 4QAFC 1TZHV 5BQBA 2GOOA 3B4VA 4UHYA 1XWDB 1BNDB 1HCFA 3MJGA 1LXIA 1RV6V 1WQ9A 5HK5A 5HHCA 4HQUA 4MQWA 1NYUB 2FJGV 5BQEA 1QFWB 1KATW 1VPPV 1S4YB 1SGFB 1WAQA 3FUBB 4BV4L 1VPFA 3S1KV 1HCNB 3KFDA 1B98A 5HHDA 3QTKA 1HRPA 3E07A 1NYSB 4YCGC 5HI4A 2H64A 4MPLA 5HI3A 2QJBA 2QJ9A 4HR9A 2ASKA 2V5EB 3SEKB 5HI5A 1E9JA 2GYZA 1B8MB 1XWDA 1MKKA 4EDWV 1HD4A 5JZ7A 4AY9B 1BNDA 4UI0A 1REUA 2H62A 5BPUA 1MJVA 2GYRA 1BMPA 2C7WA 3QB4A 1FL7B 1QFWA 4HSAA 3V6BA 5FV2V 1KLCA 1KLAA 2GNNA 2IFGE 2XV7A 4ZFFC 3BDYV 2XACA 4KXZA 5AEJA 1WWWV 1QTYR 2ARVA 1HCNA 1JPYA 2R53A 2QCWA 4LXSJ 4XPJA 4ZBNA 2KD3A 3S1BV 5E4GA 4GLSE 3BMPA 1TZIV 1CZ8V 4KV5A 2QR0C 3RJRA 1TGKA 1TGJA 4GLNE 4X1JA 4HQXA 2TGIA 4EAXA 1KTZA 1B8MA 4UI1A 5BQ8B 4UHZA 1TFGA 1SG1A 1DZ7A 4EC7A 1AGQA 5F3BC 5HHVA 1BTGA 3V2AA 1MKGA 2VWEA 3EVSB 1FL7A 3MJKA 1FZVA
chains in the Genus database with same CATH topology
3JVFA 3P9WA 3IJ2A 4KZNA 4LXRJ 1FLTV 4EFVA 4N1DA 4YCIC 5BQ8D 1LX5A 1AOCA 1ZKZA 1BJ1V 2B0UA 3HH2A 2PJYA 1ES7A 1B8KA 2VXSA 2GH0C 2FJHV 1WQ9B 2P6AA 2QCQA 4FAOA 4QHUC 4MQWB 2X1XE 4QCIC 5BQEB 1NT3A 4AY9A 5BQ8A 1M4UL 5HK5E 1PDGA 1WQ8A 2QJAA 1M4UA 3EO1C 4UI2B 5BQCA 3BK3A 1HRPB 2ARPA 3BUKA 5HHXA 4WPBA 5F3HI 2BHKA 2R52A 4MIDA 2X1WA 2VPFA 4EDXV 1BETA 5FV1V 1REWA 4QAFC 1TZHV 5BQBA 2GOOA 3B4VA 4UHYA 1XWDB 1BNDB 1HCFA 3MJGA 1LXIA 1RV6V 1WQ9A 5HK5A 5HHCA 4HQUA 4MQWA 1NYUB 2FJGV 5BQEA 1QFWB 1KATW 1VPPV 1S4YB 1SGFB 1WAQA 3FUBB 4BV4L 1VPFA 3S1KV 1HCNB 3KFDA 1B98A 5HHDA 3QTKA 1HRPA 3E07A 1NYSB 4YCGC 5HI4A 2H64A 4MPLA 5HI3A 2QJBA 2QJ9A 4HR9A 2ASKA 2V5EB 3SEKB 5HI5A 1E9JA 2GYZA 1B8MB 1XWDA 1MKKA 4EDWV 1HD4A 5JZ7A 4AY9B 1BNDA 4UI0A 1REUA 2H62A 5BPUA 1MJVA 2GYRA 1BMPA 2C7WA 3QB4A 1FL7B 1QFWA 4HSAA 3V6BA 5FV2V 1KLCA 1KLAA 2GNNA 2IFGE 2XV7A 4ZFFC 3BDYV 2XACA 4KXZA 5AEJA 1WWWV 1QTYR 2ARVA 1HCNA 1JPYA 2R53A 2QCWA 4LXSJ 4XPJA 4ZBNA 2KD3A 3S1BV 5E4GA 4GLSE 3BMPA 1TZIV 1CZ8V 4KV5A 2QR0C 3RJRA 1TGKA 1TGJA 4GLNE 4X1JA 4HQXA 2TGIA 4EAXA 1KTZA 1B8MA 4UI1A 5BQ8B 4UHZA 1TFGA 1SG1A 1DZ7A 4EC7A 1AGQA 5F3BC 5HHVA 1BTGA 3V2AA 1MKGA 2VWEA 3EVSB 1FL7A 3MJKA 1FZVA
chains in the Genus database with same CATH homology


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