4HQXA

Crystal structure of human pdgf-bb in complex with a modified nucleotide aptamer (somamer sl4)
Total Genus 11
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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
11
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 11
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 4hqxA00
3S1BV 2XACA 2B0UA 3MJGA 3EO1C 4EDWV 1REWA 2H62A 2QJ9A 4MPLA 3FUBB 3S1KV 1ES7A 3EVSB 4ZFFC 1NT3A 2QJBA 1BNDA 3JVFA 5F3HI 2IFGE 1VPFA 4KXZA 3V2AA 4N1DA 1WWWV 1TZHV 1KATW 1BJ1V 3E07A 1FL7B 5F3BC 5BQ8A 1XWDB 2VXSA 5BPUA 1AOCA 2FJHV 5HHVA 2QCWA 4KZNA 4UI0A 5HI5A 3RJRA 2C7WA 1QFWB 2V5EB 2GOOA 4EFVA 3QTKA 2X1WA 1DZ7A 3IJ2A 1KLAA 1CZ8V 2QJAA 5HHCA 1TGKA 2GNNA 1BETA 2FJGV 5HK5E 1LX5A 2VWEA 4ZBNA 4HSAA 3V6BA 1SGFB 5JZ7A 2GYRA 4WPBA 4AY9B 3BDYV 4YCIC 1B8MB 1HD4A 5HHXA 2GYZA 5FV2V 5BQEA 4EAXA 4HR9A 1ZKZA 4KV5A 1TGJA 4BV4L 1JPYA 2ARPA 4QHUC 4YCGC 3BUKA 1HCNB 4HQXA 1B8KA 1BMPA 4LXRJ 3B4VA 4MQWB 1WQ8A 3MJKA 4GLSE 2TGIA 1FL7A 4QCIC 5HK5A 1E9JA 1XWDA 2XV7A 4UI1A 1WQ9A 5HI3A 4UI2B 1HRPA 1MJVA 1HCFA 5AEJA 1M4UA 1QTYR 5HI4A 1KTZA 3KFDA 1NYUB 4EC7A 4HQUA 5BQ8D 1VPPV 4UHZA 1S4YB 1MKGA 1MKKA 1NYSB 4LXSJ 2ASKA 2P6AA 5HHDA 2R53A 2VPFA 4X1JA 5BQCA 2KD3A 5BQBA 4AY9A 1BNDB 2PJYA 1REUA 1B8MA 2BHKA 4GLNE 1SG1A 5BQEB 4QAFC 1M4UL 5BQ8B 1AGQA 2QCQA 4FAOA 1LXIA 4UHYA 1B98A 2R52A 1HCNA 4XPJA 3HH2A 1KLCA 1TFGA 1QFWA 1TZIV 2QR0C 1FZVA 4MQWA 2X1XE 3QB4A 1FLTV 5E4GA 1WQ9B 2ARVA 1PDGA 3BK3A 1WAQA 1HRPB 5FV1V 1BTGA 3SEKB 1RV6V 3BMPA 3P9WA 2H64A 4MIDA 2GH0C 4EDXV
chains in the Genus database with same CATH superfamily
3S1BV 2XACA 2B0UA 3MJGA 3EO1C 4EDWV 1REWA 2H62A 2QJ9A 4MPLA 3FUBB 3S1KV 1ES7A 3EVSB 4ZFFC 1NT3A 2QJBA 1BNDA 3JVFA 5F3HI 2IFGE 1VPFA 4KXZA 3V2AA 4N1DA 1WWWV 1TZHV 1KATW 1BJ1V 3E07A 1FL7B 5F3BC 5BQ8A 1XWDB 2VXSA 5BPUA 1AOCA 2FJHV 5HHVA 2QCWA 4KZNA 4UI0A 5HI5A 3RJRA 2C7WA 1QFWB 2V5EB 2GOOA 4EFVA 3QTKA 2X1WA 1DZ7A 3IJ2A 1KLAA 1CZ8V 2QJAA 5HHCA 1TGKA 2GNNA 1BETA 2FJGV 5HK5E 1LX5A 2VWEA 4ZBNA 4HSAA 3V6BA 1SGFB 5JZ7A 2GYRA 4WPBA 4AY9B 3BDYV 4YCIC 1B8MB 1HD4A 5HHXA 2GYZA 5FV2V 5BQEA 4EAXA 4HR9A 1ZKZA 4KV5A 1TGJA 4BV4L 1JPYA 2ARPA 4QHUC 4YCGC 3BUKA 1HCNB 4HQXA 1B8KA 1BMPA 4LXRJ 3B4VA 4MQWB 1WQ8A 3MJKA 4GLSE 2TGIA 1FL7A 4QCIC 5HK5A 1E9JA 1XWDA 2XV7A 4UI1A 1WQ9A 5HI3A 4UI2B 1HRPA 1MJVA 1HCFA 5AEJA 1M4UA 1QTYR 5HI4A 1KTZA 3KFDA 1NYUB 4EC7A 4HQUA 5BQ8D 1VPPV 4UHZA 1S4YB 1MKGA 1MKKA 1NYSB 4LXSJ 2ASKA 2P6AA 5HHDA 2R53A 2VPFA 4X1JA 5BQCA 2KD3A 5BQBA 4AY9A 1BNDB 2PJYA 1REUA 1B8MA 2BHKA 4GLNE 1SG1A 5BQEB 4QAFC 1M4UL 5BQ8B 1AGQA 2QCQA 4FAOA 1LXIA 4UHYA 1B98A 2R52A 1HCNA 4XPJA 3HH2A 1KLCA 1TFGA 1QFWA 1TZIV 2QR0C 1FZVA 4MQWA 2X1XE 3QB4A 1FLTV 5E4GA 1WQ9B 2ARVA 1PDGA 3BK3A 1WAQA 1HRPB 5FV1V 1BTGA 3SEKB 1RV6V 3BMPA 3P9WA 2H64A 4MIDA 2GH0C 4EDXV
chains in the Genus database with same CATH topology
3S1BV 2XACA 2B0UA 3MJGA 3EO1C 4EDWV 1REWA 2H62A 2QJ9A 4MPLA 3FUBB 3S1KV 1ES7A 3EVSB 4ZFFC 1NT3A 2QJBA 1BNDA 3JVFA 5F3HI 2IFGE 1VPFA 4KXZA 3V2AA 4N1DA 1WWWV 1TZHV 1KATW 1BJ1V 3E07A 1FL7B 5F3BC 5BQ8A 1XWDB 2VXSA 5BPUA 1AOCA 2FJHV 5HHVA 2QCWA 4KZNA 4UI0A 5HI5A 3RJRA 2C7WA 1QFWB 2V5EB 2GOOA 4EFVA 3QTKA 2X1WA 1DZ7A 3IJ2A 1KLAA 1CZ8V 2QJAA 5HHCA 1TGKA 2GNNA 1BETA 2FJGV 5HK5E 1LX5A 2VWEA 4ZBNA 4HSAA 3V6BA 1SGFB 5JZ7A 2GYRA 4WPBA 4AY9B 3BDYV 4YCIC 1B8MB 1HD4A 5HHXA 2GYZA 5FV2V 5BQEA 4EAXA 4HR9A 1ZKZA 4KV5A 1TGJA 4BV4L 1JPYA 2ARPA 4QHUC 4YCGC 3BUKA 1HCNB 4HQXA 1B8KA 1BMPA 4LXRJ 3B4VA 4MQWB 1WQ8A 3MJKA 4GLSE 2TGIA 1FL7A 4QCIC 5HK5A 1E9JA 1XWDA 2XV7A 4UI1A 1WQ9A 5HI3A 4UI2B 1HRPA 1MJVA 1HCFA 5AEJA 1M4UA 1QTYR 5HI4A 1KTZA 3KFDA 1NYUB 4EC7A 4HQUA 5BQ8D 1VPPV 4UHZA 1S4YB 1MKGA 1MKKA 1NYSB 4LXSJ 2ASKA 2P6AA 5HHDA 2R53A 2VPFA 4X1JA 5BQCA 2KD3A 5BQBA 4AY9A 1BNDB 2PJYA 1REUA 1B8MA 2BHKA 4GLNE 1SG1A 5BQEB 4QAFC 1M4UL 5BQ8B 1AGQA 2QCQA 4FAOA 1LXIA 4UHYA 1B98A 2R52A 1HCNA 4XPJA 3HH2A 1KLCA 1TFGA 1QFWA 1TZIV 2QR0C 1FZVA 4MQWA 2X1XE 3QB4A 1FLTV 5E4GA 1WQ9B 2ARVA 1PDGA 3BK3A 1WAQA 1HRPB 5FV1V 1BTGA 3SEKB 1RV6V 3BMPA 3P9WA 2H64A 4MIDA 2GH0C 4EDXV
chains in the Genus database with same CATH homology


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