5J3PA

Crystal structure of the catalytic domain of human tyrosyl dna phosphodiesterase 2
Total Genus 59
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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
59
sequence length
250
structure length
246
Chain Sequence
HMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLESTRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNLRDREVTRSGGLPNNIVDVWEFLGKPKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAHIIPRSLDLLGLEKLDCGRFPSDHWGLLCNLDII
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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 Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
pubmed doi rcsb
molecule tags Hydrolase
source organism Homo sapiens
molecule keywords Tyrosyl-DNA phosphodiesterase 2
total genus 59
structure length 246
sequence length 250
chains with identical sequence B
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 5j3pA00
3MTCA 2DDTA 5CFGA 1ZWXA 5INPA 2ISIA 1HD7A 2O3CA 5J3PA 2JC4A 2F2FB 1E9NA 1AKOA 1BIXA 2F1NA 1YJHA 2V0SA 5DG0A 3CJCD 2A42B 3G3YA 4B5GA 4LNDA 4L1ZA 4C1RA 4FVAA 3G8VA 4CMNA 3G3CA 5J3ZA 4FPVA 1DE8A 2A41B 1DNKA 4B5MA 5J42A 5INKA 3G38A 5DFHA 3G2CA 4IEMA 4GYZA 2J63A 3WCXA 1SR4B 4B5FA 3I5VA 4AWNA 3N9VA 2XSWA 2A3ZB 4F1RA 5A7IA 3G6SA 1WDUA 3L1WA 2DNJA 4A9CA 2D1KB 4GEWA 3G4TA 1VYBA 4L1YA 3I46A 3NR8A 2JC5A 5INLA 4K6LF 5INQA 2VOAA 2UYRX 5DFJA 4GZ2A 3I48A 5INNA 4QHEA 2A40B 3GA6A 5EWTA 3MPRA 3G0RA 3W3DB 1DE9A 4F1HA 3TEBA 3W2YA 3U8UA 3G00A 4QHDA 1I9YA 1SI6X 4GZ0A 2V0RA 2O3HA 3G91A 5CFEA 1NTFA 4L20A 3G1KA 4GZ1A 2IMQX 4JG3A 5J3SA 3G2DA 5DV2A 1DEWA 2DDSA 4F1HB 3NGNA 4F1IA 3NGQA 3I41A 5INMA 3G0AA 1ATND 3DNIA 3FZIA 3K55A 2DDRA 3NGOA 5J8NA 4B5JA 5DFIA 2EI9A 3W2XA 4B5IA 4CMLA 5A7JA 4RUWA 5DFFA 5DV4A 5INOA 4B5HA 5HT2A 4L21A 4QH9A 1I9ZA 4PUQA 1Y21A
chains in the Genus database with same CATH superfamily
3MTCA 2DDTA 5CFGA 1ZWXA 5INPA 2ISIA 1HD7A 2O3CA 5J3PA 2JC4A 2F2FB 1E9NA 1AKOA 1BIXA 2F1NA 1YJHA 2V0SA 5DG0A 3CJCD 2A42B 3G3YA 4B5GA 4LNDA 4L1ZA 4C1RA 4FVAA 3G8VA 4CMNA 3G3CA 5J3ZA 4FPVA 1DE8A 2A41B 1DNKA 4B5MA 5J42A 5INKA 3G38A 5DFHA 3G2CA 4IEMA 4GYZA 2J63A 3WCXA 1SR4B 4B5FA 3I5VA 4AWNA 3N9VA 2XSWA 2A3ZB 4F1RA 5A7IA 3G6SA 1WDUA 3L1WA 2DNJA 4A9CA 2D1KB 4GEWA 3G4TA 1VYBA 4L1YA 3I46A 3NR8A 2JC5A 5INLA 4K6LF 5INQA 2VOAA 2UYRX 5DFJA 4GZ2A 3I48A 5INNA 4QHEA 2A40B 3GA6A 5EWTA 3MPRA 3G0RA 3W3DB 1DE9A 4F1HA 3TEBA 3W2YA 3U8UA 3G00A 4QHDA 1I9YA 1SI6X 4GZ0A 2V0RA 2O3HA 3G91A 5CFEA 1NTFA 4L20A 3G1KA 4GZ1A 2IMQX 4JG3A 5J3SA 3G2DA 5DV2A 1DEWA 2DDSA 4F1HB 3NGNA 4F1IA 3NGQA 3I41A 5INMA 3G0AA 1ATND 3DNIA 3FZIA 3K55A 2DDRA 3NGOA 5J8NA 4B5JA 5DFIA 2EI9A 3W2XA 4B5IA 4CMLA 5A7JA 4RUWA 5DFFA 5DV4A 5INOA 4B5HA 5HT2A 4L21A 4QH9A 1I9ZA 4PUQA 1Y21A
chains in the Genus database with same CATH topology
3MTCA 2DDTA 5CFGA 1ZWXA 5INPA 2ISIA 1HD7A 2O3CA 5J3PA 2JC4A 2F2FB 1E9NA 1AKOA 1BIXA 2F1NA 1YJHA 2V0SA 5DG0A 3CJCD 2A42B 3G3YA 4B5GA 4LNDA 4L1ZA 4C1RA 4FVAA 3G8VA 4CMNA 3G3CA 5J3ZA 4FPVA 1DE8A 2A41B 1DNKA 4B5MA 5J42A 5INKA 3G38A 5DFHA 3G2CA 4IEMA 4GYZA 2J63A 3WCXA 1SR4B 4B5FA 3I5VA 4AWNA 3N9VA 2XSWA 2A3ZB 4F1RA 5A7IA 3G6SA 1WDUA 3L1WA 2DNJA 4A9CA 2D1KB 4GEWA 3G4TA 1VYBA 4L1YA 3I46A 3NR8A 2JC5A 5INLA 4K6LF 5INQA 2VOAA 2UYRX 5DFJA 4GZ2A 3I48A 5INNA 4QHEA 2A40B 3GA6A 5EWTA 3MPRA 3G0RA 3W3DB 1DE9A 4F1HA 3TEBA 3W2YA 3U8UA 3G00A 4QHDA 1I9YA 1SI6X 4GZ0A 2V0RA 2O3HA 3G91A 5CFEA 1NTFA 4L20A 3G1KA 4GZ1A 2IMQX 4JG3A 5J3SA 3G2DA 5DV2A 1DEWA 2DDSA 4F1HB 3NGNA 4F1IA 3NGQA 3I41A 5INMA 3G0AA 1ATND 3DNIA 3FZIA 3K55A 2DDRA 3NGOA 5J8NA 4B5JA 5DFIA 2EI9A 3W2XA 4B5IA 4CMLA 5A7JA 4RUWA 5DFFA 5DV4A 5INOA 4B5HA 5HT2A 4L21A 4QH9A 1I9ZA 4PUQA 1Y21A
chains in the Genus database with same CATH homology


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