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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publication title Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
pubmed doi rcsb
molecule tags Hydrolase/dna
source organism Danio rerio
molecule keywords Tyrosyl-DNA phosphodiesterase 2
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
4GZ2A 4B5GA 4LNDA 5DG0A 2JC4A 5CFGA 4QHDA 1SI6X 4IEMA 1I9YA 4K6LF 2DDSA 2O3HA 3G2CA 1Y21A 3L1WA 4F1RA 4GEWA 3G91A 3NGOA 1YJHA 2V0RA 2A40B 3G1KA 2DNJA 3MTCA 3G0AA 3NR8A 3DNIA 1BIXA 2XSWA 5J8NA 4GZ0A 5DV2A 1DNKA 4FVAA 5INMA 3I46A 3WCXA 1I9ZA 4F1HA 3G8VA 3G0RA 1ATND 3GA6A 2DDRA 1DEWA 5HT2A 3W2YA 3G2DA 4B5HA 4A9CA 3CJCD 4L1ZA 4CMNA 3K55A 3G38A 3TEBA 3G6SA 1WDUA 3G3CA 5INPA 3MPRA 5INNA 3I41A 5EWTA 5J3PA 4AWNA 2JC5A 5INQA 3I5VA 1AKOA 2D1KB 5A7JA 4L21A 3W3DB 4B5IA 4B5FA 4PUQA 4B5MA 2DDTA 4JG3A 1HD7A 1NTFA 5INOA 3N9VA 2UYRX 5INKA 3I48A 4L1YA 5J3SA 2ISIA 2A41B 2F1NA 5A7IA 4QHEA 4F1HB 4L20A 1DE9A 4FPVA 1ZWXA 4B5JA 5CFEA 3FZIA 2V0SA 2J63A 2O3CA 4QH9A 3NGQA 3W2XA 4F1IA 3G3YA 5DFIA 4RUWA 5J3ZA 5DFFA 3G4TA 2F2FB 2EI9A 5DFJA 4C1RA 1VYBA 1E9NA 1SR4B 3U8UA 5J42A 5INLA 2A42B 2VOAA 5DV4A 2A3ZB 1DE8A 4GZ1A 3NGNA 4GYZA 4CMLA 3G00A 2IMQX 5DFHA
chains in the Genus database with same CATH superfamily
4GZ2A 4B5GA 4LNDA 5DG0A 2JC4A 5CFGA 4QHDA 1SI6X 4IEMA 1I9YA 4K6LF 2DDSA 2O3HA 3G2CA 1Y21A 3L1WA 4F1RA 4GEWA 3G91A 3NGOA 1YJHA 2V0RA 2A40B 3G1KA 2DNJA 3MTCA 3G0AA 3NR8A 3DNIA 1BIXA 2XSWA 5J8NA 4GZ0A 5DV2A 1DNKA 4FVAA 5INMA 3I46A 3WCXA 1I9ZA 4F1HA 3G8VA 3G0RA 1ATND 3GA6A 2DDRA 1DEWA 5HT2A 3W2YA 3G2DA 4B5HA 4A9CA 3CJCD 4L1ZA 4CMNA 3K55A 3G38A 3TEBA 3G6SA 1WDUA 3G3CA 5INPA 3MPRA 5INNA 3I41A 5EWTA 5J3PA 4AWNA 2JC5A 5INQA 3I5VA 1AKOA 2D1KB 5A7JA 4L21A 3W3DB 4B5IA 4B5FA 4PUQA 4B5MA 2DDTA 4JG3A 1HD7A 1NTFA 5INOA 3N9VA 2UYRX 5INKA 3I48A 4L1YA 5J3SA 2ISIA 2A41B 2F1NA 5A7IA 4QHEA 4F1HB 4L20A 1DE9A 4FPVA 1ZWXA 4B5JA 5CFEA 3FZIA 2V0SA 2J63A 2O3CA 4QH9A 3NGQA 3W2XA 4F1IA 3G3YA 5DFIA 4RUWA 5J3ZA 5DFFA 3G4TA 2F2FB 2EI9A 5DFJA 4C1RA 1VYBA 1E9NA 1SR4B 3U8UA 5J42A 5INLA 2A42B 2VOAA 5DV4A 2A3ZB 1DE8A 4GZ1A 3NGNA 4GYZA 4CMLA 3G00A 2IMQX 5DFHA
chains in the Genus database with same CATH topology
4GZ2A 4B5GA 4LNDA 5DG0A 2JC4A 5CFGA 4QHDA 1SI6X 4IEMA 1I9YA 4K6LF 2DDSA 2O3HA 3G2CA 1Y21A 3L1WA 4F1RA 4GEWA 3G91A 3NGOA 1YJHA 2V0RA 2A40B 3G1KA 2DNJA 3MTCA 3G0AA 3NR8A 3DNIA 1BIXA 2XSWA 5J8NA 4GZ0A 5DV2A 1DNKA 4FVAA 5INMA 3I46A 3WCXA 1I9ZA 4F1HA 3G8VA 3G0RA 1ATND 3GA6A 2DDRA 1DEWA 5HT2A 3W2YA 3G2DA 4B5HA 4A9CA 3CJCD 4L1ZA 4CMNA 3K55A 3G38A 3TEBA 3G6SA 1WDUA 3G3CA 5INPA 3MPRA 5INNA 3I41A 5EWTA 5J3PA 4AWNA 2JC5A 5INQA 3I5VA 1AKOA 2D1KB 5A7JA 4L21A 3W3DB 4B5IA 4B5FA 4PUQA 4B5MA 2DDTA 4JG3A 1HD7A 1NTFA 5INOA 3N9VA 2UYRX 5INKA 3I48A 4L1YA 5J3SA 2ISIA 2A41B 2F1NA 5A7IA 4QHEA 4F1HB 4L20A 1DE9A 4FPVA 1ZWXA 4B5JA 5CFEA 3FZIA 2V0SA 2J63A 2O3CA 4QH9A 3NGQA 3W2XA 4F1IA 3G3YA 5DFIA 4RUWA 5J3ZA 5DFFA 3G4TA 2F2FB 2EI9A 5DFJA 4C1RA 1VYBA 1E9NA 1SR4B 3U8UA 5J42A 5INLA 2A42B 2VOAA 5DV4A 2A3ZB 1DE8A 4GZ1A 3NGNA 4GYZA 4CMLA 3G00A 2IMQX 5DFHA
chains in the Genus database with same CATH homology


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

 
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#similar chains, but unknotted
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