4FPVA

Crystal structure of d. rerio tdp2 complexed with single strand dna product
Total Genus 77

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
77
sequence length
250
structure length
250
Chain Sequence
DSKLSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQELIPAYVQYLKKRAVSYLFFEGSDDGYFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQKLYLMTSHLESCKNQSQERTKQLRVVLQKIKEAPEDAIVIFAGDTNLRDAEVANVGGLPAGVCDVWEQLGKQEHCRYTWDTKANSNKTVPYVSRCRFDRIFLRSAKTAPPVTPDHMALIGMEKLDCGRYTSDHWGIYCTFNT

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
EMPTYS6 (216-224)TI1 (131-134)TVIII1 (132-135)AH1 (138-152)TIV2 (211-214)S5 (198-207)TVIII2 (154-157)S2 (156-162)AH2 (164-173)S3 (177-181)S4 (188-194)TI6 (239-242)TI5 (208-211)AH3 (242-259)TIV3 (223-226)S7 (227-235)S1 (122-129)TII1 (135-138)TI2 (174-177)Updating...
connected with : NaN
molecule tags Hydrolase/dna
source organism Danio rerio
publication title Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
pubmed doi rcsb
molecule keywords Tyrosyl-DNA phosphodiesterase 2
total genus 77
structure length 250
sequence length 250
chains with identical sequence B
ec nomenclature ec 3.1.4.-:
pdb deposition date 2012-06-22

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 4fpvA00
3TEBA 4K6LF 3L1WA 4PUQA 3G0RA 3G91A 4C1RA 3I41A 5INQA 3G3YA 2F2FB 3G1KA 3W2XA 5J42A 4QHEA 5J3SA 4QH9A 2DDRA 4IEMA 4FPVA 5INPA 3MPRA 4GEWA 3NGOA 3WCXA 1HD7A 2ISIA 4B5FA 5CFGA 5A7JA 2UYRX 5CFEA 4CMLA 1YJHA 1I9YA 3GA6A 5INLA 2XSWA 4F1HB 2A40B 4AWNA 3K55A 3I48A 3G4TA 4B5HA 3NR8A 2A42B 5HT2A 1DE8A 1AKOA 1NTFA 4F1IA 3N9VA 2V0SA 4GYZA 1ZWXA 5DFHA 5INKA 3I46A 2JC4A 3MTCA 2O3CA 3W2YA 4L1ZA 5DFJA 4GZ2A 5J8NA 5DFFA 2JC5A 2F1NA 3G0AA 2DDTA 4LNDA 4F1HA 2D1KB 5EWTA 2V0RA 3NGNA 2J63A 1WDUA 4B5GA 3I5VA 2A3ZB 3G2DA 3G38A 4GZ0A 1E9NA 2DDSA 1DEWA 1DNKA 1ATND 4L21A 2DNJA 4B5MA 1SR4B 1Y21A 2A41B 3DNIA 2IMQX 4L20A 3G3CA 3CJCD 5DV2A 4B5JA 1I9ZA 4A9CA 3G6SA 4F1RA 1BIXA 4L1YA 4FVAA 4RUWA 1DE9A 2EI9A 4B5IA 3G8VA 5J3ZA 2VOAA 3NGQA 3FZIA 5J3PA 2O3HA 3U8UA 5DV4A 4CMNA 3G00A 4QHDA 4GZ1A 3W3DB 5DFIA 1SI6X 3G2CA 5DG0A 4JG3A 5INMA 5INOA 5INNA 5A7IA 1VYBA
chains in the Genus database with same CATH superfamily
3TEBA 4K6LF 3L1WA 4PUQA 3G0RA 3G91A 4C1RA 3I41A 5INQA 3G3YA 2F2FB 3G1KA 3W2XA 5J42A 4QHEA 5J3SA 4QH9A 2DDRA 4IEMA 4FPVA 5INPA 3MPRA 4GEWA 3NGOA 3WCXA 1HD7A 2ISIA 4B5FA 5CFGA 5A7JA 2UYRX 5CFEA 4CMLA 1YJHA 1I9YA 3GA6A 5INLA 2XSWA 4F1HB 2A40B 4AWNA 3K55A 3I48A 3G4TA 4B5HA 3NR8A 2A42B 5HT2A 1DE8A 1AKOA 1NTFA 4F1IA 3N9VA 2V0SA 4GYZA 1ZWXA 5DFHA 5INKA 3I46A 2JC4A 3MTCA 2O3CA 3W2YA 4L1ZA 5DFJA 4GZ2A 5J8NA 5DFFA 2JC5A 2F1NA 3G0AA 2DDTA 4LNDA 4F1HA 2D1KB 5EWTA 2V0RA 3NGNA 2J63A 1WDUA 4B5GA 3I5VA 2A3ZB 3G2DA 3G38A 4GZ0A 1E9NA 2DDSA 1DEWA 1DNKA 1ATND 4L21A 2DNJA 4B5MA 1SR4B 1Y21A 2A41B 3DNIA 2IMQX 4L20A 3G3CA 3CJCD 5DV2A 4B5JA 1I9ZA 4A9CA 3G6SA 4F1RA 1BIXA 4L1YA 4FVAA 4RUWA 1DE9A 2EI9A 4B5IA 3G8VA 5J3ZA 2VOAA 3NGQA 3FZIA 5J3PA 2O3HA 3U8UA 5DV4A 4CMNA 3G00A 4QHDA 4GZ1A 3W3DB 5DFIA 1SI6X 3G2CA 5DG0A 4JG3A 5INMA 5INOA 5INNA 5A7IA 1VYBA
chains in the Genus database with same CATH topology
3TEBA 4K6LF 3L1WA 4PUQA 3G0RA 3G91A 4C1RA 3I41A 5INQA 3G3YA 2F2FB 3G1KA 3W2XA 5J42A 4QHEA 5J3SA 4QH9A 2DDRA 4IEMA 4FPVA 5INPA 3MPRA 4GEWA 3NGOA 3WCXA 1HD7A 2ISIA 4B5FA 5CFGA 5A7JA 2UYRX 5CFEA 4CMLA 1YJHA 1I9YA 3GA6A 5INLA 2XSWA 4F1HB 2A40B 4AWNA 3K55A 3I48A 3G4TA 4B5HA 3NR8A 2A42B 5HT2A 1DE8A 1AKOA 1NTFA 4F1IA 3N9VA 2V0SA 4GYZA 1ZWXA 5DFHA 5INKA 3I46A 2JC4A 3MTCA 2O3CA 3W2YA 4L1ZA 5DFJA 4GZ2A 5J8NA 5DFFA 2JC5A 2F1NA 3G0AA 2DDTA 4LNDA 4F1HA 2D1KB 5EWTA 2V0RA 3NGNA 2J63A 1WDUA 4B5GA 3I5VA 2A3ZB 3G2DA 3G38A 4GZ0A 1E9NA 2DDSA 1DEWA 1DNKA 1ATND 4L21A 2DNJA 4B5MA 1SR4B 1Y21A 2A41B 3DNIA 2IMQX 4L20A 3G3CA 3CJCD 5DV2A 4B5JA 1I9ZA 4A9CA 3G6SA 4F1RA 1BIXA 4L1YA 4FVAA 4RUWA 1DE9A 2EI9A 4B5IA 3G8VA 5J3ZA 2VOAA 3NGQA 3FZIA 5J3PA 2O3HA 3U8UA 5DV4A 4CMNA 3G00A 4QHDA 4GZ1A 3W3DB 5DFIA 1SI6X 3G2CA 5DG0A 4JG3A 5INMA 5INOA 5INNA 5A7IA 1VYBA
chains in the Genus database with same CATH homology


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