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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

Application loaded.