5J3SA

Crystal structure of the catalytic domain of human tyrosyl dna phosphodiesterase 2 in complex with a small molecule inhibitor
Total Genus 56

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

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
AH3 (234-249)EMPTYAH1 (129-143)S1 (114-120)TI1 (122-125)TIV1 (123-126)S2 (147-153)TIV4 (202-205)TIV3 (199-202)TI2 (165-168)S5 (189-198)S3 (168-172)S4 (179-185)TI3 (185-188)S7 (221-225)TI4 (230-233)TII1 (126-129)AH2 (155-164)S6 (207-215)Updating...
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
3I5VA 4JG3A 2JC4A 3CJCD 5DFHA 2V0SA 1VYBA 3MPRA 4B5HA 4FVAA 5INLA 4CMNA 3W2YA 5J42A 3G3YA 5INPA 4GZ0A 2ISIA 5J8NA 5J3PA 5INKA 2JC5A 3G38A 2DDTA 2DDSA 5J3ZA 1I9ZA 2XSWA 3NR8A 1I9YA 1Y21A 3G6SA 2F2FB 2D1KB 3G8VA 4GEWA 1NTFA 4F1IA 2J63A 1DEWA 4PUQA 5HT2A 5DFJA 4FPVA 5DG0A 4AWNA 3W2XA 2A42B 4GZ1A 4L21A 2EI9A 3GA6A 5A7JA 1SR4B 1E9NA 3W3DB 5INQA 3NGQA 2A40B 1DE8A 3K55A 4GYZA 5DV4A 3U8UA 5J3SA 3G0RA 4K6LF 1WDUA 1YJHA 2VOAA 4LNDA 5INNA 3G2CA 3I46A 2UYRX 3FZIA 1DE9A 5DV2A 4F1HA 4QHDA 2DNJA 4B5MA 3NGNA 3DNIA 4QH9A 4B5IA 4GZ2A 3L1WA 4F1RA 3G4TA 2A41B 2A3ZB 4B5GA 4C1RA 2O3HA 5INOA 5A7IA 1SI6X 5CFGA 3N9VA 4L20A 2V0RA 3TEBA 3I48A 4RUWA 1ZWXA 4B5JA 4L1ZA 2IMQX 1HD7A 1BIXA 1AKOA 5CFEA 5EWTA 4B5FA 4A9CA 3G91A 2O3CA 3G0AA 4F1HB 3G00A 2DDRA 4CMLA 5INMA 5DFFA 3G2DA 4IEMA 4L1YA 4QHEA 3NGOA 1DNKA 3G1KA 5DFIA 3WCXA 3MTCA 2F1NA 1ATND 3I41A 3G3CA
chains in the Genus database with same CATH superfamily
3I5VA 4JG3A 2JC4A 3CJCD 5DFHA 2V0SA 1VYBA 3MPRA 4B5HA 4FVAA 5INLA 4CMNA 3W2YA 5J42A 3G3YA 5INPA 4GZ0A 2ISIA 5J8NA 5J3PA 5INKA 2JC5A 3G38A 2DDTA 2DDSA 5J3ZA 1I9ZA 2XSWA 3NR8A 1I9YA 1Y21A 3G6SA 2F2FB 2D1KB 3G8VA 4GEWA 1NTFA 4F1IA 2J63A 1DEWA 4PUQA 5HT2A 5DFJA 4FPVA 5DG0A 4AWNA 3W2XA 2A42B 4GZ1A 4L21A 2EI9A 3GA6A 5A7JA 1SR4B 1E9NA 3W3DB 5INQA 3NGQA 2A40B 1DE8A 3K55A 4GYZA 5DV4A 3U8UA 5J3SA 3G0RA 4K6LF 1WDUA 1YJHA 2VOAA 4LNDA 5INNA 3G2CA 3I46A 2UYRX 3FZIA 1DE9A 5DV2A 4F1HA 4QHDA 2DNJA 4B5MA 3NGNA 3DNIA 4QH9A 4B5IA 4GZ2A 3L1WA 4F1RA 3G4TA 2A41B 2A3ZB 4B5GA 4C1RA 2O3HA 5INOA 5A7IA 1SI6X 5CFGA 3N9VA 4L20A 2V0RA 3TEBA 3I48A 4RUWA 1ZWXA 4B5JA 4L1ZA 2IMQX 1HD7A 1BIXA 1AKOA 5CFEA 5EWTA 4B5FA 4A9CA 3G91A 2O3CA 3G0AA 4F1HB 3G00A 2DDRA 4CMLA 5INMA 5DFFA 3G2DA 4IEMA 4L1YA 4QHEA 3NGOA 1DNKA 3G1KA 5DFIA 3WCXA 3MTCA 2F1NA 1ATND 3I41A 3G3CA
chains in the Genus database with same CATH topology
3I5VA 4JG3A 2JC4A 3CJCD 5DFHA 2V0SA 1VYBA 3MPRA 4B5HA 4FVAA 5INLA 4CMNA 3W2YA 5J42A 3G3YA 5INPA 4GZ0A 2ISIA 5J8NA 5J3PA 5INKA 2JC5A 3G38A 2DDTA 2DDSA 5J3ZA 1I9ZA 2XSWA 3NR8A 1I9YA 1Y21A 3G6SA 2F2FB 2D1KB 3G8VA 4GEWA 1NTFA 4F1IA 2J63A 1DEWA 4PUQA 5HT2A 5DFJA 4FPVA 5DG0A 4AWNA 3W2XA 2A42B 4GZ1A 4L21A 2EI9A 3GA6A 5A7JA 1SR4B 1E9NA 3W3DB 5INQA 3NGQA 2A40B 1DE8A 3K55A 4GYZA 5DV4A 3U8UA 5J3SA 3G0RA 4K6LF 1WDUA 1YJHA 2VOAA 4LNDA 5INNA 3G2CA 3I46A 2UYRX 3FZIA 1DE9A 5DV2A 4F1HA 4QHDA 2DNJA 4B5MA 3NGNA 3DNIA 4QH9A 4B5IA 4GZ2A 3L1WA 4F1RA 3G4TA 2A41B 2A3ZB 4B5GA 4C1RA 2O3HA 5INOA 5A7IA 1SI6X 5CFGA 3N9VA 4L20A 2V0RA 3TEBA 3I48A 4RUWA 1ZWXA 4B5JA 4L1ZA 2IMQX 1HD7A 1BIXA 1AKOA 5CFEA 5EWTA 4B5FA 4A9CA 3G91A 2O3CA 3G0AA 4F1HB 3G00A 2DDRA 4CMLA 5INMA 5DFFA 3G2DA 4IEMA 4L1YA 4QHEA 3NGOA 1DNKA 3G1KA 5DFIA 3WCXA 3MTCA 2F1NA 1ATND 3I41A 3G3CA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3I5V A;  4JG3 A;  2JC4 A;  3CJC D;  5DFH A;  2V0S A;  1VYB A;  3MPR A;  4B5H A;  4FVA A;  5INL A;  4CMN A;  3W2Y A;  5J42 A;  3G3Y A;  5INP A;  4GZ0 A;  2ISI A;  5J8N A;  5J3P A;  5INK A;  2JC5 A;  3G38 A;  2DDT A;  2DDS A;  5J3Z A;  1I9Z A;  2XSW A;  3NR8 A;  1I9Y A;  1Y21 A;  3G6S A;  2F2F B;  2D1K B;  3G8V A;  4GEW A;  1NTF A;  4F1I A;  2J63 A;  1DEW A;  4PUQ A;  5HT2 A;  5DFJ A;  4FPV A;  5DG0 A;  4AWN A;  3W2X A;  2A42 B;  4GZ1 A;  4L21 A;  2EI9 A;  3GA6 A;  5A7J A;  1SR4 B;  1E9N A;  3W3D B;  5INQ A;  3NGQ A;  2A40 B;  1DE8 A;  3K55 A;  4GYZ A;  5DV4 A;  3U8U A;  5J3S A;  3G0R A;  4K6L F;  1WDU A;  1YJH A;  2VOA A;  4LND A;  5INN A;  3G2C A;  3I46 A;  2UYR X;  3FZI A;  1DE9 A;  5DV2 A;  4F1H A;  4QHD A;  2DNJ A;  4B5M A;  3NGN A;  3DNI A;  4QH9 A;  4B5I A;  4GZ2 A;  3L1W A;  4F1R A;  3G4T A;  2A41 B;  2A3Z B;  4B5G A;  4C1R A;  2O3H A;  5INO A;  5A7I A;  1SI6 X;  5CFG A;  3N9V A;  4L20 A;  2V0R A;  3TEB A;  3I48 A;  4RUW A;  1ZWX A;  4B5J A;  4L1Z A;  2IMQ X;  1HD7 A;  1BIX A;  1AKO A;  5CFE A;  5EWT A;  4B5F A;  4A9C A;  3G91 A;  2O3C A;  3G0A A;  4F1H B;  3G00 A;  2DDR A;  4CML A;  5INM A;  5DFF A;  3G2D A;  4IEM A;  4L1Y A;  4QHE A;  3NGO A;  1DNK A;  3G1K A;  5DFI A;  3WCX A;  3MTC A;  2F1N A;  1ATN D;  3I41 A;  3G3C A; 
#chains in the Genus database with same CATH topology
 3I5V A;  4JG3 A;  2JC4 A;  3CJC D;  5DFH A;  2V0S A;  1VYB A;  3MPR A;  4B5H A;  4FVA A;  5INL A;  4CMN A;  3W2Y A;  5J42 A;  3G3Y A;  5INP A;  4GZ0 A;  2ISI A;  5J8N A;  5J3P A;  5INK A;  2JC5 A;  3G38 A;  2DDT A;  2DDS A;  5J3Z A;  1I9Z A;  2XSW A;  3NR8 A;  1I9Y A;  1Y21 A;  3G6S A;  2F2F B;  2D1K B;  3G8V A;  4GEW A;  1NTF A;  4F1I A;  2J63 A;  1DEW A;  4PUQ A;  5HT2 A;  5DFJ A;  4FPV A;  5DG0 A;  4AWN A;  3W2X A;  2A42 B;  4GZ1 A;  4L21 A;  2EI9 A;  3GA6 A;  5A7J A;  1SR4 B;  1E9N A;  3W3D B;  5INQ A;  3NGQ A;  2A40 B;  1DE8 A;  3K55 A;  4GYZ A;  5DV4 A;  3U8U A;  5J3S A;  3G0R A;  4K6L F;  1WDU A;  1YJH A;  2VOA A;  4LND A;  5INN A;  3G2C A;  3I46 A;  2UYR X;  3FZI A;  1DE9 A;  5DV2 A;  4F1H A;  4QHD A;  2DNJ A;  4B5M A;  3NGN A;  3DNI A;  4QH9 A;  4B5I A;  4GZ2 A;  3L1W A;  4F1R A;  3G4T A;  2A41 B;  2A3Z B;  4B5G A;  4C1R A;  2O3H A;  5INO A;  5A7I A;  1SI6 X;  5CFG A;  3N9V A;  4L20 A;  2V0R A;  3TEB A;  3I48 A;  4RUW A;  1ZWX A;  4B5J A;  4L1Z A;  2IMQ X;  1HD7 A;  1BIX A;  1AKO A;  5CFE A;  5EWT A;  4B5F A;  4A9C A;  3G91 A;  2O3C A;  3G0A A;  4F1H B;  3G00 A;  2DDR A;  4CML A;  5INM A;  5DFF A;  3G2D A;  4IEM A;  4L1Y A;  4QHE A;  3NGO A;  1DNK A;  3G1K A;  5DFI A;  3WCX A;  3MTC A;  2F1N A;  1ATN D;  3I41 A;  3G3C A; 
#chains in the Genus database with same CATH homology
 3I5V A;  4JG3 A;  2JC4 A;  3CJC D;  5DFH A;  2V0S A;  1VYB A;  3MPR A;  4B5H A;  4FVA A;  5INL A;  4CMN A;  3W2Y A;  5J42 A;  3G3Y A;  5INP A;  4GZ0 A;  2ISI A;  5J8N A;  5J3P A;  5INK A;  2JC5 A;  3G38 A;  2DDT A;  2DDS A;  5J3Z A;  1I9Z A;  2XSW A;  3NR8 A;  1I9Y A;  1Y21 A;  3G6S A;  2F2F B;  2D1K B;  3G8V A;  4GEW A;  1NTF A;  4F1I A;  2J63 A;  1DEW A;  4PUQ A;  5HT2 A;  5DFJ A;  4FPV A;  5DG0 A;  4AWN A;  3W2X A;  2A42 B;  4GZ1 A;  4L21 A;  2EI9 A;  3GA6 A;  5A7J A;  1SR4 B;  1E9N A;  3W3D B;  5INQ A;  3NGQ A;  2A40 B;  1DE8 A;  3K55 A;  4GYZ A;  5DV4 A;  3U8U A;  5J3S A;  3G0R A;  4K6L F;  1WDU A;  1YJH A;  2VOA A;  4LND A;  5INN A;  3G2C A;  3I46 A;  2UYR X;  3FZI A;  1DE9 A;  5DV2 A;  4F1H A;  4QHD A;  2DNJ A;  4B5M A;  3NGN A;  3DNI A;  4QH9 A;  4B5I A;  4GZ2 A;  3L1W A;  4F1R A;  3G4T A;  2A41 B;  2A3Z B;  4B5G A;  4C1R A;  2O3H A;  5INO A;  5A7I A;  1SI6 X;  5CFG A;  3N9V A;  4L20 A;  2V0R A;  3TEB A;  3I48 A;  4RUW A;  1ZWX A;  4B5J A;  4L1Z A;  2IMQ X;  1HD7 A;  1BIX A;  1AKO A;  5CFE A;  5EWT A;  4B5F A;  4A9C A;  3G91 A;  2O3C A;  3G0A A;  4F1H B;  3G00 A;  2DDR A;  4CML A;  5INM A;  5DFF A;  3G2D A;  4IEM A;  4L1Y A;  4QHE A;  3NGO A;  1DNK A;  3G1K A;  5DFI A;  3WCX A;  3MTC A;  2F1N A;  1ATN D;  3I41 A;  3G3C A; 
4GYZA 4GZ0A 4GZ1A 4PUQA 5HT2A 5INOA 5J3SA 5J3ZA 5J42A
similar chains in the Genus database (40% sequence similarity)
None
similar chains in the pdb database (40% sequence similarity)

 
#similar chains in the Genus database (40% sequence similarity)
4GYZ A; 4GZ0 A; 4GZ1 A; 4PUQ A; 5HT2 A; 5INO A; 5J3S A; 5J3Z A; 5J42 A; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)


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