5INKA

Mouse tdp2 reaction product (5'-phosphorylated dna)-abasic/thf-mg2+ complex
Total Genus 81
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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
81
sequence length
254
structure length
254
Chain Sequence
GLEDSSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRAASYTIITGNEEGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNEFCLMTSHLESTREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGGLPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLVGLEKLDCGRFPSDHWGLLCTLNVVL
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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 Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2.
pubmed doi rcsb
molecule tags Hydrolase/dna
source organism Mus musculus
molecule keywords Tyrosyl-DNA phosphodiesterase 2
total genus 81
structure length 254
sequence length 254
chains with identical sequence B
ec nomenclature ec 3.1.4.-:
pdb deposition date 2016-03-07

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 5inkA00
4F1RA 4LNDA 4GYZA 4B5HA 3MPRA 5J42A 3NGQA 4JG3A 3GA6A 4GEWA 4L1ZA 1SR4B 2D1KB 4QH9A 3I46A 4C1RA 3G3CA 2A3ZB 2VOAA 5INLA 5DG0A 2XSWA 1ATND 5INOA 4FPVA 3I48A 1YJHA 3MTCA 1ZWXA 2A40B 3G3YA 4B5GA 5DFIA 1DEWA 3NR8A 3K55A 1AKOA 2V0RA 4GZ1A 4A9CA 5CFGA 2DDSA 2A42B 4F1HB 1Y21A 4B5JA 3G8VA 3G0AA 4QHEA 2JC5A 4K6LF 4IEMA 1WDUA 5J8NA 2O3CA 5CFEA 4GZ2A 2A41B 4CMNA 1I9ZA 5DFJA 2ISIA 5DV2A 1DE8A 2O3HA 3I41A 2UYRX 4B5IA 3FZIA 1DNKA 4L21A 1VYBA 2JC4A 5DFFA 3G91A 3DNIA 3G38A 4RUWA 3N9VA 5EWTA 5INQA 4F1HA 2DDRA 3G00A 5J3ZA 5INKA 3WCXA 3G4TA 4CMLA 4B5FA 3CJCD 4L1YA 3L1WA 3G1KA 2F1NA 5A7IA 5HT2A 2F2FB 1E9NA 3G0RA 4FVAA 4F1IA 1DE9A 3U8UA 5A7JA 2DNJA 1HD7A 3NGOA 5J3SA 5INNA 3W3DB 5J3PA 3NGNA 3G2CA 5DFHA 4L20A 5INPA 3W2XA 1SI6X 2DDTA 2IMQX 2J63A 3TEBA 4QHDA 5DV4A 4AWNA 2V0SA 1I9YA 3I5VA 5INMA 3G2DA 4GZ0A 1BIXA 4PUQA 1NTFA 4B5MA 3G6SA 3W2YA 2EI9A
chains in the Genus database with same CATH superfamily
4F1RA 4LNDA 4GYZA 4B5HA 3MPRA 5J42A 3NGQA 4JG3A 3GA6A 4GEWA 4L1ZA 1SR4B 2D1KB 4QH9A 3I46A 4C1RA 3G3CA 2A3ZB 2VOAA 5INLA 5DG0A 2XSWA 1ATND 5INOA 4FPVA 3I48A 1YJHA 3MTCA 1ZWXA 2A40B 3G3YA 4B5GA 5DFIA 1DEWA 3NR8A 3K55A 1AKOA 2V0RA 4GZ1A 4A9CA 5CFGA 2DDSA 2A42B 4F1HB 1Y21A 4B5JA 3G8VA 3G0AA 4QHEA 2JC5A 4K6LF 4IEMA 1WDUA 5J8NA 2O3CA 5CFEA 4GZ2A 2A41B 4CMNA 1I9ZA 5DFJA 2ISIA 5DV2A 1DE8A 2O3HA 3I41A 2UYRX 4B5IA 3FZIA 1DNKA 4L21A 1VYBA 2JC4A 5DFFA 3G91A 3DNIA 3G38A 4RUWA 3N9VA 5EWTA 5INQA 4F1HA 2DDRA 3G00A 5J3ZA 5INKA 3WCXA 3G4TA 4CMLA 4B5FA 3CJCD 4L1YA 3L1WA 3G1KA 2F1NA 5A7IA 5HT2A 2F2FB 1E9NA 3G0RA 4FVAA 4F1IA 1DE9A 3U8UA 5A7JA 2DNJA 1HD7A 3NGOA 5J3SA 5INNA 3W3DB 5J3PA 3NGNA 3G2CA 5DFHA 4L20A 5INPA 3W2XA 1SI6X 2DDTA 2IMQX 2J63A 3TEBA 4QHDA 5DV4A 4AWNA 2V0SA 1I9YA 3I5VA 5INMA 3G2DA 4GZ0A 1BIXA 4PUQA 1NTFA 4B5MA 3G6SA 3W2YA 2EI9A
chains in the Genus database with same CATH topology
4F1RA 4LNDA 4GYZA 4B5HA 3MPRA 5J42A 3NGQA 4JG3A 3GA6A 4GEWA 4L1ZA 1SR4B 2D1KB 4QH9A 3I46A 4C1RA 3G3CA 2A3ZB 2VOAA 5INLA 5DG0A 2XSWA 1ATND 5INOA 4FPVA 3I48A 1YJHA 3MTCA 1ZWXA 2A40B 3G3YA 4B5GA 5DFIA 1DEWA 3NR8A 3K55A 1AKOA 2V0RA 4GZ1A 4A9CA 5CFGA 2DDSA 2A42B 4F1HB 1Y21A 4B5JA 3G8VA 3G0AA 4QHEA 2JC5A 4K6LF 4IEMA 1WDUA 5J8NA 2O3CA 5CFEA 4GZ2A 2A41B 4CMNA 1I9ZA 5DFJA 2ISIA 5DV2A 1DE8A 2O3HA 3I41A 2UYRX 4B5IA 3FZIA 1DNKA 4L21A 1VYBA 2JC4A 5DFFA 3G91A 3DNIA 3G38A 4RUWA 3N9VA 5EWTA 5INQA 4F1HA 2DDRA 3G00A 5J3ZA 5INKA 3WCXA 3G4TA 4CMLA 4B5FA 3CJCD 4L1YA 3L1WA 3G1KA 2F1NA 5A7IA 5HT2A 2F2FB 1E9NA 3G0RA 4FVAA 4F1IA 1DE9A 3U8UA 5A7JA 2DNJA 1HD7A 3NGOA 5J3SA 5INNA 3W3DB 5J3PA 3NGNA 3G2CA 5DFHA 4L20A 5INPA 3W2XA 1SI6X 2DDTA 2IMQX 2J63A 3TEBA 4QHDA 5DV4A 4AWNA 2V0SA 1I9YA 3I5VA 5INMA 3G2DA 4GZ0A 1BIXA 4PUQA 1NTFA 4B5MA 3G6SA 3W2YA 2EI9A
chains in the Genus database with same CATH homology


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