5J3SA

Crystal structure of the catalytic domain of human tyrosyl dna phosphodiesterase 2 in complex with a small molecule inhibitor
Total Genus 56
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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
56
sequence length
248
structure length
236
Chain Sequence
HMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAVIFAGDTNLRDREVTRSGGLPNNIVDVWEFLGKPKHCQYTWDTQMNSNLGITAACKLRFDRIFFRIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLD
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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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connected with : NaN
molecule tags Hydrolase
source organism Homo sapiens
publication title Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
pubmed doi rcsb
molecule keywords Tyrosyl-DNA phosphodiesterase 2
total genus 56
structure length 236
sequence length 248
ec nomenclature ec 3.1.4.-:
pdb deposition date 2016-03-31

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 5j3sA00
2A41B 5J42A 4B5JA 4L1YA 4GZ0A 2DDRA 3NR8A 3TEBA 5INMA 4B5MA 1ZWXA 2A3ZB 5DV2A 5EWTA 2DNJA 2F2FB 5DFIA 5DFJA 4GZ1A 5DV4A 1ATND 3G2CA 3I41A 1VYBA 4L21A 3NGQA 3U8UA 3W3DB 2O3HA 4LNDA 1NTFA 3MTCA 4B5IA 3NGNA 2JC4A 4L20A 5INLA 1E9NA 3G91A 5INQA 4QHDA 4CMNA 1I9YA 2A42B 4PUQA 2A40B 1HD7A 4B5HA 1Y21A 1I9ZA 3FZIA 4GEWA 1YJHA 3G2DA 4AWNA 3G0AA 3G1KA 3WCXA 2O3CA 2DDTA 3N9VA 4F1RA 2V0RA 2DDSA 4QH9A 4JG3A 2J63A 3G3CA 5DG0A 4F1HA 3W2YA 3G8VA 1SI6X 3G3YA 4IEMA 3GA6A 5HT2A 4F1HB 3G00A 4GZ2A 1AKOA 2D1KB 4L1ZA 2ISIA 3G38A 4F1IA 2UYRX 5J3ZA 4K6LF 3G0RA 2F1NA 4GYZA 1SR4B 5J8NA 4FVAA 2VOAA 3I5VA 4RUWA 1DE9A 5DFFA 1BIXA 3CJCD 2EI9A 2XSWA 4B5FA 4B5GA 4CMLA 1DEWA 2JC5A 3K55A 4FPVA 4A9CA 5DFHA 1DE8A 3NGOA 3MPRA 3I46A 4QHEA 3I48A 1WDUA 5INPA 3W2XA 3G6SA 4C1RA 5A7JA 1DNKA 3G4TA 5INOA 2V0SA 5J3SA 5J3PA 5A7IA 3DNIA 5INNA 5INKA 3L1WA 5CFGA 2IMQX 5CFEA
chains in the Genus database with same CATH superfamily
2A41B 5J42A 4B5JA 4L1YA 4GZ0A 2DDRA 3NR8A 3TEBA 5INMA 4B5MA 1ZWXA 2A3ZB 5DV2A 5EWTA 2DNJA 2F2FB 5DFIA 5DFJA 4GZ1A 5DV4A 1ATND 3G2CA 3I41A 1VYBA 4L21A 3NGQA 3U8UA 3W3DB 2O3HA 4LNDA 1NTFA 3MTCA 4B5IA 3NGNA 2JC4A 4L20A 5INLA 1E9NA 3G91A 5INQA 4QHDA 4CMNA 1I9YA 2A42B 4PUQA 2A40B 1HD7A 4B5HA 1Y21A 1I9ZA 3FZIA 4GEWA 1YJHA 3G2DA 4AWNA 3G0AA 3G1KA 3WCXA 2O3CA 2DDTA 3N9VA 4F1RA 2V0RA 2DDSA 4QH9A 4JG3A 2J63A 3G3CA 5DG0A 4F1HA 3W2YA 3G8VA 1SI6X 3G3YA 4IEMA 3GA6A 5HT2A 4F1HB 3G00A 4GZ2A 1AKOA 2D1KB 4L1ZA 2ISIA 3G38A 4F1IA 2UYRX 5J3ZA 4K6LF 3G0RA 2F1NA 4GYZA 1SR4B 5J8NA 4FVAA 2VOAA 3I5VA 4RUWA 1DE9A 5DFFA 1BIXA 3CJCD 2EI9A 2XSWA 4B5FA 4B5GA 4CMLA 1DEWA 2JC5A 3K55A 4FPVA 4A9CA 5DFHA 1DE8A 3NGOA 3MPRA 3I46A 4QHEA 3I48A 1WDUA 5INPA 3W2XA 3G6SA 4C1RA 5A7JA 1DNKA 3G4TA 5INOA 2V0SA 5J3SA 5J3PA 5A7IA 3DNIA 5INNA 5INKA 3L1WA 5CFGA 2IMQX 5CFEA
chains in the Genus database with same CATH topology
2A41B 5J42A 4B5JA 4L1YA 4GZ0A 2DDRA 3NR8A 3TEBA 5INMA 4B5MA 1ZWXA 2A3ZB 5DV2A 5EWTA 2DNJA 2F2FB 5DFIA 5DFJA 4GZ1A 5DV4A 1ATND 3G2CA 3I41A 1VYBA 4L21A 3NGQA 3U8UA 3W3DB 2O3HA 4LNDA 1NTFA 3MTCA 4B5IA 3NGNA 2JC4A 4L20A 5INLA 1E9NA 3G91A 5INQA 4QHDA 4CMNA 1I9YA 2A42B 4PUQA 2A40B 1HD7A 4B5HA 1Y21A 1I9ZA 3FZIA 4GEWA 1YJHA 3G2DA 4AWNA 3G0AA 3G1KA 3WCXA 2O3CA 2DDTA 3N9VA 4F1RA 2V0RA 2DDSA 4QH9A 4JG3A 2J63A 3G3CA 5DG0A 4F1HA 3W2YA 3G8VA 1SI6X 3G3YA 4IEMA 3GA6A 5HT2A 4F1HB 3G00A 4GZ2A 1AKOA 2D1KB 4L1ZA 2ISIA 3G38A 4F1IA 2UYRX 5J3ZA 4K6LF 3G0RA 2F1NA 4GYZA 1SR4B 5J8NA 4FVAA 2VOAA 3I5VA 4RUWA 1DE9A 5DFFA 1BIXA 3CJCD 2EI9A 2XSWA 4B5FA 4B5GA 4CMLA 1DEWA 2JC5A 3K55A 4FPVA 4A9CA 5DFHA 1DE8A 3NGOA 3MPRA 3I46A 4QHEA 3I48A 1WDUA 5INPA 3W2XA 3G6SA 4C1RA 5A7JA 1DNKA 3G4TA 5INOA 2V0SA 5J3SA 5J3PA 5A7IA 3DNIA 5INNA 5INKA 3L1WA 5CFGA 2IMQX 5CFEA
chains in the Genus database with same CATH homology


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