1JY1A

Crystal structure of human tyrosyl-dna phosphodiesterase (tdp1)
Total Genus 137
Loading diagram...

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
137
sequence length
464
structure length
439
Chain Sequence
LEDPGEGQDIWDMLDKGNPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHAAESWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGSVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
Loading diagram...

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
{{ tooltip.sname }} connected with {{ tooltip.tname }} : {{qFormat(tooltip.svalue) }}
publication title The crystal structure of human tyrosyl-DNA phosphodiesterase, Tdp1.
pubmed doi rcsb
molecule tags Hydrolase
source organism Homo sapiens
molecule keywords TYROSYL-DNA PHOSPHODIESTERASE
total genus 137
structure length 439
sequence length 464
ec nomenclature
pdb deposition date 2001-09-10

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF06087 Tyr-DNA_phospho Tyrosyl-DNA phosphodiesterase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.30.870.10 Alpha Beta 2-Layer Sandwich Endonuclease; Chain A Endonuclease Chain A 1jy1A01
3.30.870.20 Alpha Beta 2-Layer Sandwich Endonuclease; Chain A Phospholipase D/nuclease; domain 2 1jy1A02
1V0RA 1XDPA 1V0VA 2F5TX 1Q32A 1RGTA 2C1LA 1F0IA 4GGJA 1RGUA 4GEMA 5BQTA 1NOPA 1MU7A 1XDOA 5BPIA 3HSIA 2O8RA 3SQ3A 3SQ8A 2ZE9A 4RCTA 1RFIA 3QPHA 1V0WA 1QZQA 4GGKA 1JY1A 4GENA 3SQ5A 1RG2A 1V0UA 3SQ7A 1V0SA 4H4AA 1RFFA 1V0YA 4URJA 1BYRA 4GELA 5LZKA 5BOXA 1RH0A 1BYSA 2ZE4A 1V0TA 1MU9A 1RG1A 5BPDA
chains in the Genus database with same CATH superfamily
1V0RA 1XDPA 1V0VA 2F5TX 1Q32A 3R3PA 2C1LA 1F0IA 4GGJA 1RGTA 1RGUA 4GEMA 5BQTA 1NOPA 1MU7A 1XDOA 5BPIA 3HSIA 2O8RA 3SQ3A 3SQ8A 2ZE9A 4RCTA 1RFIA 3QPHA 1V0WA 1QZQA 4GGKA 1JY1A 2YMBA 4GENA 3SQ5A 1RG2A 1V0UA 3SQ7A 1V0SA 4H4AA 1ODGA 1RFFA 1V0YA 4URJA 1CW0A 1BYRA 4GELA 3HRLA 5LZKA 1VSRA 4A5ZA 5BOXA 1RH0A 1BYSA 2ZE4A 1V0TA 1MU9A 1RG1A 5BPDA
chains in the Genus database with same CATH topology
1V0RA 1XDPA 1V0VA 2F5TX 1Q32A 1RGTA 2C1LA 1F0IA 4GGJA 1RGUA 4GEMA 5BQTA 1NOPA 1MU7A 1XDOA 5BPIA 3HSIA 2O8RA 3SQ3A 3SQ8A 2ZE9A 4RCTA 1RFIA 3QPHA 1V0WA 1QZQA 4GGKA 1JY1A 4GENA 3SQ5A 1RG2A 1V0UA 3SQ7A 1V0SA 4H4AA 1RFFA 1V0YA 4URJA 1BYRA 4GELA 5LZKA 5BOXA 1RH0A 1BYSA 2ZE4A 1V0TA 1MU9A 1RG1A 5BPDA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1V0R A;  1XDP A;  1V0V A;  2F5T X;  1Q32 A;  1RGT A;  2C1L A;  1F0I A;  4GGJ A;  1RGU A;  4GEM A;  5BQT A;  1NOP A;  1MU7 A;  1XDO A;  5BPI A;  3HSI A;  2O8R A;  3SQ3 A;  3SQ8 A;  2ZE9 A;  4RCT A;  1RFI A;  3QPH A;  1V0W A;  1QZQ A;  4GGK A;  1JY1 A;  4GEN A;  3SQ5 A;  1RG2 A;  1V0U A;  3SQ7 A;  1V0S A;  4H4A A;  1RFF A;  1V0Y A;  4URJ A;  1BYR A;  4GEL A;  5LZK A;  5BOX A;  1RH0 A;  1BYS A;  2ZE4 A;  1V0T A;  1MU9 A;  1RG1 A;  5BPD A; 
#chains in the Genus database with same CATH topology
 1V0R A;  1XDP A;  1V0V A;  2F5T X;  1Q32 A;  3R3P A;  2C1L A;  1F0I A;  4GGJ A;  1RGT A;  1RGU A;  4GEM A;  5BQT A;  1NOP A;  1MU7 A;  1XDO A;  5BPI A;  3HSI A;  2O8R A;  3SQ3 A;  3SQ8 A;  2ZE9 A;  4RCT A;  1RFI A;  3QPH A;  1V0W A;  1QZQ A;  4GGK A;  1JY1 A;  2YMB A;  4GEN A;  3SQ5 A;  1RG2 A;  1V0U A;  3SQ7 A;  1V0S A;  4H4A A;  1ODG A;  1RFF A;  1V0Y A;  4URJ A;  1CW0 A;  1BYR A;  4GEL A;  3HRL A;  5LZK A;  1VSR A;  4A5Z A;  5BOX A;  1RH0 A;  1BYS A;  2ZE4 A;  1V0T A;  1MU9 A;  1RG1 A;  5BPD A; 
#chains in the Genus database with same CATH homology
 1V0R A;  1XDP A;  1V0V A;  2F5T X;  1Q32 A;  1RGT A;  2C1L A;  1F0I A;  4GGJ A;  1RGU A;  4GEM A;  5BQT A;  1NOP A;  1MU7 A;  1XDO A;  5BPI A;  3HSI A;  2O8R A;  3SQ3 A;  3SQ8 A;  2ZE9 A;  4RCT A;  1RFI A;  3QPH A;  1V0W A;  1QZQ A;  4GGK A;  1JY1 A;  4GEN A;  3SQ5 A;  1RG2 A;  1V0U A;  3SQ7 A;  1V0S A;  4H4A A;  1RFF A;  1V0Y A;  4URJ A;  1BYR A;  4GEL A;  5LZK A;  5BOX A;  1RH0 A;  1BYS A;  2ZE4 A;  1V0T A;  1MU9 A;  1RG1 A;  5BPD 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...