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


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