4FPVA

Crystal structure of d. rerio tdp2 complexed with single strand dna product
Total Genus 77
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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
77
sequence length
250
structure length
250
Chain Sequence
DSKLSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQELIPAYVQYLKKRAVSYLFFEGSDDGYFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQKLYLMTSHLESCKNQSQERTKQLRVVLQKIKEAPEDAIVIFAGDTNLRDAEVANVGGLPAGVCDVWEQLGKQEHCRYTWDTKANSNKTVPYVSRCRFDRIFLRSAKTAPPVTPDHMALIGMEKLDCGRYTSDHWGIYCTFNT
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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 Hydrolase/dna
molecule keywords Tyrosyl-DNA phosphodiesterase 2
publication title Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
pubmed doi rcsb
source organism Danio rerio
total genus 77
structure length 250
sequence length 250
chains with identical sequence B
ec nomenclature ec 3.1.4.-:
pdb deposition date 2012-06-22

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF03372 Exo_endo_phos Endonuclease/Exonuclease/phosphatase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.60.10.10 Alpha Beta 4-Layer Sandwich Deoxyribonuclease I; Chain A Endonuclease/exonuclease/phosphatase 4fpvA00
4F1IA 3GA6A 3G00A 1DE9A 1VYBA 1SR4B 5CFEA 4A9CA 2D1KB 2JC4A 3G8VA 3I41A 3G6SA 4GYZA 2J63A 2VOAA 1DEWA 4B5HA 3G91A 5DV4A 2XSWA 1ZWXA 4GZ0A 5J3PA 3K55A 3G2DA 3I5VA 3W2YA 4RUWA 3W2XA 4C1RA 5J42A 2F1NA 5DFIA 5DFFA 2DDRA 2A42B 4LNDA 3MTCA 2O3CA 3MPRA 2F2FB 2O3HA 4F1RA 2IMQX 3G1KA 3I48A 3N9VA 4CMLA 1Y21A 3G3CA 4B5GA 3CJCD 5HT2A 1I9YA 2EI9A 5DG0A 2JC5A 4CMNA 4L1YA 3G0AA 3DNIA 4AWNA 5DFJA 4B5JA 5INKA 5J8NA 4GZ1A 4L20A 1WDUA 4F1HB 4K6LF 1DE8A 3G38A 5INMA 4B5IA 3G4TA 3G0RA 5EWTA 4FVAA 3TEBA 2UYRX 2DDSA 2ISIA 4GEWA 1YJHA 4F1HA 4QHDA 1NTFA 1SI6X 3NGQA 4QH9A 2DNJA 3W3DB 4L1ZA 5INOA 2A3ZB 5DV2A 2V0SA 1I9ZA 3WCXA 5INNA 4B5FA 1DNKA 1HD7A 1E9NA 2V0RA 4FPVA 4JG3A 4GZ2A 2DDTA 4IEMA 4B5MA 5DFHA 1ATND 4QHEA 5J3SA 5INLA 5INPA 3G3YA 3NR8A 5CFGA 3NGOA 5A7JA 3U8UA 3L1WA 5INQA 5A7IA 2A41B 3FZIA 3G2CA 5J3ZA 1BIXA 1AKOA 4PUQA 3I46A 2A40B 4L21A 3NGNA
chains in the Genus database with same CATH superfamily
4F1IA 3GA6A 3G00A 1DE9A 1VYBA 1SR4B 5CFEA 4A9CA 2D1KB 2JC4A 3G8VA 3I41A 3G6SA 4GYZA 2J63A 2VOAA 1DEWA 4B5HA 3G91A 5DV4A 2XSWA 1ZWXA 4GZ0A 5J3PA 3K55A 3G2DA 3I5VA 3W2YA 4RUWA 3W2XA 4C1RA 5J42A 2F1NA 5DFIA 5DFFA 2DDRA 2A42B 4LNDA 3MTCA 2O3CA 3MPRA 2F2FB 2O3HA 4F1RA 2IMQX 3G1KA 3I48A 3N9VA 4CMLA 1Y21A 3G3CA 4B5GA 3CJCD 5HT2A 1I9YA 2EI9A 5DG0A 2JC5A 4CMNA 4L1YA 3G0AA 3DNIA 4AWNA 5DFJA 4B5JA 5INKA 5J8NA 4GZ1A 4L20A 1WDUA 4F1HB 4K6LF 1DE8A 3G38A 5INMA 4B5IA 3G4TA 3G0RA 5EWTA 4FVAA 3TEBA 2UYRX 2DDSA 2ISIA 4GEWA 1YJHA 4F1HA 4QHDA 1NTFA 1SI6X 3NGQA 4QH9A 2DNJA 3W3DB 4L1ZA 5INOA 2A3ZB 5DV2A 2V0SA 1I9ZA 3WCXA 5INNA 4B5FA 1DNKA 1HD7A 1E9NA 2V0RA 4FPVA 4JG3A 4GZ2A 2DDTA 4IEMA 4B5MA 5DFHA 1ATND 4QHEA 5J3SA 5INLA 5INPA 3G3YA 3NR8A 5CFGA 3NGOA 5A7JA 3U8UA 3L1WA 5INQA 5A7IA 2A41B 3FZIA 3G2CA 5J3ZA 1BIXA 1AKOA 4PUQA 3I46A 2A40B 4L21A 3NGNA
chains in the Genus database with same CATH topology
4F1IA 3GA6A 3G00A 1DE9A 1VYBA 1SR4B 5CFEA 4A9CA 2D1KB 2JC4A 3G8VA 3I41A 3G6SA 4GYZA 2J63A 2VOAA 1DEWA 4B5HA 3G91A 5DV4A 2XSWA 1ZWXA 4GZ0A 5J3PA 3K55A 3G2DA 3I5VA 3W2YA 4RUWA 3W2XA 4C1RA 5J42A 2F1NA 5DFIA 5DFFA 2DDRA 2A42B 4LNDA 3MTCA 2O3CA 3MPRA 2F2FB 2O3HA 4F1RA 2IMQX 3G1KA 3I48A 3N9VA 4CMLA 1Y21A 3G3CA 4B5GA 3CJCD 5HT2A 1I9YA 2EI9A 5DG0A 2JC5A 4CMNA 4L1YA 3G0AA 3DNIA 4AWNA 5DFJA 4B5JA 5INKA 5J8NA 4GZ1A 4L20A 1WDUA 4F1HB 4K6LF 1DE8A 3G38A 5INMA 4B5IA 3G4TA 3G0RA 5EWTA 4FVAA 3TEBA 2UYRX 2DDSA 2ISIA 4GEWA 1YJHA 4F1HA 4QHDA 1NTFA 1SI6X 3NGQA 4QH9A 2DNJA 3W3DB 4L1ZA 5INOA 2A3ZB 5DV2A 2V0SA 1I9ZA 3WCXA 5INNA 4B5FA 1DNKA 1HD7A 1E9NA 2V0RA 4FPVA 4JG3A 4GZ2A 2DDTA 4IEMA 4B5MA 5DFHA 1ATND 4QHEA 5J3SA 5INLA 5INPA 3G3YA 3NR8A 5CFGA 3NGOA 5A7JA 3U8UA 3L1WA 5INQA 5A7IA 2A41B 3FZIA 3G2CA 5J3ZA 1BIXA 1AKOA 4PUQA 3I46A 2A40B 4L21A 3NGNA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4F1I A;  3GA6 A;  3G00 A;  1DE9 A;  1VYB A;  1SR4 B;  5CFE A;  4A9C A;  2D1K B;  2JC4 A;  3G8V A;  3I41 A;  3G6S A;  4GYZ A;  2J63 A;  2VOA A;  1DEW A;  4B5H A;  3G91 A;  5DV4 A;  2XSW A;  1ZWX A;  4GZ0 A;  5J3P A;  3K55 A;  3G2D A;  3I5V A;  3W2Y A;  4RUW A;  3W2X A;  4C1R A;  5J42 A;  2F1N A;  5DFI A;  5DFF A;  2DDR A;  2A42 B;  4LND A;  3MTC A;  2O3C A;  3MPR A;  2F2F B;  2O3H A;  4F1R A;  2IMQ X;  3G1K A;  3I48 A;  3N9V A;  4CML A;  1Y21 A;  3G3C A;  4B5G A;  3CJC D;  5HT2 A;  1I9Y A;  2EI9 A;  5DG0 A;  2JC5 A;  4CMN A;  4L1Y A;  3G0A A;  3DNI A;  4AWN A;  5DFJ A;  4B5J A;  5INK A;  5J8N A;  4GZ1 A;  4L20 A;  1WDU A;  4F1H B;  4K6L F;  1DE8 A;  3G38 A;  5INM A;  4B5I A;  3G4T A;  3G0R A;  5EWT A;  4FVA A;  3TEB A;  2UYR X;  2DDS A;  2ISI A;  4GEW A;  1YJH A;  4F1H A;  4QHD A;  1NTF A;  1SI6 X;  3NGQ A;  4QH9 A;  2DNJ A;  3W3D B;  4L1Z A;  5INO A;  2A3Z B;  5DV2 A;  2V0S A;  1I9Z A;  3WCX A;  5INN A;  4B5F A;  1DNK A;  1HD7 A;  1E9N A;  2V0R A;  4FPV A;  4JG3 A;  4GZ2 A;  2DDT A;  4IEM A;  4B5M A;  5DFH A;  1ATN D;  4QHE A;  5J3S A;  5INL A;  5INP A;  3G3Y A;  3NR8 A;  5CFG A;  3NGO A;  5A7J A;  3U8U A;  3L1W A;  5INQ A;  5A7I A;  2A41 B;  3FZI A;  3G2C A;  5J3Z A;  1BIX A;  1AKO A;  4PUQ A;  3I46 A;  2A40 B;  4L21 A;  3NGN A; 
#chains in the Genus database with same CATH topology
 4F1I A;  3GA6 A;  3G00 A;  1DE9 A;  1VYB A;  1SR4 B;  5CFE A;  4A9C A;  2D1K B;  2JC4 A;  3G8V A;  3I41 A;  3G6S A;  4GYZ A;  2J63 A;  2VOA A;  1DEW A;  4B5H A;  3G91 A;  5DV4 A;  2XSW A;  1ZWX A;  4GZ0 A;  5J3P A;  3K55 A;  3G2D A;  3I5V A;  3W2Y A;  4RUW A;  3W2X A;  4C1R A;  5J42 A;  2F1N A;  5DFI A;  5DFF A;  2DDR A;  2A42 B;  4LND A;  3MTC A;  2O3C A;  3MPR A;  2F2F B;  2O3H A;  4F1R A;  2IMQ X;  3G1K A;  3I48 A;  3N9V A;  4CML A;  1Y21 A;  3G3C A;  4B5G A;  3CJC D;  5HT2 A;  1I9Y A;  2EI9 A;  5DG0 A;  2JC5 A;  4CMN A;  4L1Y A;  3G0A A;  3DNI A;  4AWN A;  5DFJ A;  4B5J A;  5INK A;  5J8N A;  4GZ1 A;  4L20 A;  1WDU A;  4F1H B;  4K6L F;  1DE8 A;  3G38 A;  5INM A;  4B5I A;  3G4T A;  3G0R A;  5EWT A;  4FVA A;  3TEB A;  2UYR X;  2DDS A;  2ISI A;  4GEW A;  1YJH A;  4F1H A;  4QHD A;  1NTF A;  1SI6 X;  3NGQ A;  4QH9 A;  2DNJ A;  3W3D B;  4L1Z A;  5INO A;  2A3Z B;  5DV2 A;  2V0S A;  1I9Z A;  3WCX A;  5INN A;  4B5F A;  1DNK A;  1HD7 A;  1E9N A;  2V0R A;  4FPV A;  4JG3 A;  4GZ2 A;  2DDT A;  4IEM A;  4B5M A;  5DFH A;  1ATN D;  4QHE A;  5J3S A;  5INL A;  5INP A;  3G3Y A;  3NR8 A;  5CFG A;  3NGO A;  5A7J A;  3U8U A;  3L1W A;  5INQ A;  5A7I A;  2A41 B;  3FZI A;  3G2C A;  5J3Z A;  1BIX A;  1AKO A;  4PUQ A;  3I46 A;  2A40 B;  4L21 A;  3NGN A; 
#chains in the Genus database with same CATH homology
 4F1I A;  3GA6 A;  3G00 A;  1DE9 A;  1VYB A;  1SR4 B;  5CFE A;  4A9C A;  2D1K B;  2JC4 A;  3G8V A;  3I41 A;  3G6S A;  4GYZ A;  2J63 A;  2VOA A;  1DEW A;  4B5H A;  3G91 A;  5DV4 A;  2XSW A;  1ZWX A;  4GZ0 A;  5J3P A;  3K55 A;  3G2D A;  3I5V A;  3W2Y A;  4RUW A;  3W2X A;  4C1R A;  5J42 A;  2F1N A;  5DFI A;  5DFF A;  2DDR A;  2A42 B;  4LND A;  3MTC A;  2O3C A;  3MPR A;  2F2F B;  2O3H A;  4F1R A;  2IMQ X;  3G1K A;  3I48 A;  3N9V A;  4CML A;  1Y21 A;  3G3C A;  4B5G A;  3CJC D;  5HT2 A;  1I9Y A;  2EI9 A;  5DG0 A;  2JC5 A;  4CMN A;  4L1Y A;  3G0A A;  3DNI A;  4AWN A;  5DFJ A;  4B5J A;  5INK A;  5J8N A;  4GZ1 A;  4L20 A;  1WDU A;  4F1H B;  4K6L F;  1DE8 A;  3G38 A;  5INM A;  4B5I A;  3G4T A;  3G0R A;  5EWT A;  4FVA A;  3TEB A;  2UYR X;  2DDS A;  2ISI A;  4GEW A;  1YJH A;  4F1H A;  4QHD A;  1NTF A;  1SI6 X;  3NGQ A;  4QH9 A;  2DNJ A;  3W3D B;  4L1Z A;  5INO A;  2A3Z B;  5DV2 A;  2V0S A;  1I9Z A;  3WCX A;  5INN A;  4B5F A;  1DNK A;  1HD7 A;  1E9N A;  2V0R A;  4FPV A;  4JG3 A;  4GZ2 A;  2DDT A;  4IEM A;  4B5M A;  5DFH A;  1ATN D;  4QHE A;  5J3S A;  5INL A;  5INP A;  3G3Y A;  3NR8 A;  5CFG A;  3NGO A;  5A7J A;  3U8U A;  3L1W A;  5INQ A;  5A7I A;  2A41 B;  3FZI A;  3G2C A;  5J3Z A;  1BIX A;  1AKO A;  4PUQ A;  3I46 A;  2A40 B;  4L21 A;  3NGN 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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