1NOPA

Crystal structure of human tyrosyl-dna phosphodiesterase (tdp1) in complex with vanadate, dna and a human topoisomerase i-derived peptide
Total Genus 143
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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
143
sequence length
447
structure length
425
Chain Sequence
NPFQFYLTRVSGVKPKYNSGALHIKDILSPLFGTLVSSAQFNYCFDVDWLVKQYPPEFRKKPILLVHGDKREAKAHLHAQAKPYENISLCQAKLDIAFGTHHTKMMLLLYEEGLRVVIHTSNLIHADWHQKTQGIWLSPLYPRIADGTHKSGESPTHFKANLISYLTAYNAPSLKEWIDVIHKHDLSETNVYLIGSTPGRFQGSQKDNWGHFRLKKLLKDHASSMSWPVVGQFSSVGSLGADESKWLCSEFKESMLTLGVPLYLIYPSVENVRTSLEGYPAGGSLPYSIQTAEKQNWLHSYFHKWSAETSGRSNAMPHIKTYMRPSPDFSKIAWFLVTSANLSKAAWGALEKNGTQLMIRSYELGVLFLPSALGLDSFKVKQKFATFPVPYDLPPELYGSKDRPWIWNIPYVKAPDTHGNMWVPS
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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
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publication title Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide
pubmed doi rcsb
molecule tags Hydrolase/dna
source organism Homo sapiens
molecule keywords 5'-D(*AP*GP*AP*GP*TP*T)-3'
total genus 143
structure length 425
sequence length 447
chains with identical sequence B
ec nomenclature
pdb deposition date 2003-01-16

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 1nopA01
3.30.870.20 Alpha Beta 2-Layer Sandwich Endonuclease; Chain A Phospholipase D/nuclease; domain 2 1nopA02
1BYSA 1V0UA 3SQ7A 3SQ5A 1RGUA 2F5TX 4GGKA 5BPDA 5BPIA 4GEMA 3HSIA 5BQTA 1MU7A 4GENA 1RGTA 3SQ3A 3QPHA 5BOXA 2O8RA 4GELA 4RCTA 1V0RA 1V0WA 2ZE4A 1RG1A 1V0VA 1F0IA 4GGJA 1RFIA 1RH0A 1V0YA 1RG2A 5LZKA 1QZQA 1V0TA 4H4AA 1BYRA 1NOPA 1XDOA 1RFFA 2C1LA 2ZE9A 1XDPA 3SQ8A 4URJA 1Q32A 1V0SA 1MU9A 1JY1A
chains in the Genus database with same CATH superfamily
1BYSA 1V0UA 3SQ7A 3SQ5A 1RGUA 2F5TX 4GGKA 1ODGA 5BPDA 1CW0A 5BPIA 4GEMA 3HSIA 5BQTA 1MU7A 4GENA 1RGTA 3SQ3A 3QPHA 1VSRA 5BOXA 2O8RA 4GELA 4RCTA 1V0RA 1V0WA 2YMBA 2ZE4A 1RG1A 1V0VA 1F0IA 4GGJA 1RFIA 1RH0A 1V0YA 4A5ZA 1RG2A 3HRLA 3R3PA 5LZKA 1QZQA 1V0TA 4H4AA 1BYRA 1NOPA 1XDOA 1RFFA 2C1LA 2ZE9A 1XDPA 3SQ8A 4URJA 1Q32A 1V0SA 1MU9A 1JY1A
chains in the Genus database with same CATH topology
1BYSA 1V0UA 3SQ7A 3SQ5A 1RGUA 2F5TX 4GGKA 5BPDA 5BPIA 4GEMA 3HSIA 5BQTA 1MU7A 4GENA 1RGTA 3SQ3A 3QPHA 5BOXA 2O8RA 4GELA 4RCTA 1V0RA 1V0WA 2ZE4A 1RG1A 1V0VA 1F0IA 4GGJA 1RFIA 1RH0A 1V0YA 1RG2A 5LZKA 1QZQA 1V0TA 4H4AA 1BYRA 1NOPA 1XDOA 1RFFA 2C1LA 2ZE9A 1XDPA 3SQ8A 4URJA 1Q32A 1V0SA 1MU9A 1JY1A
chains in the Genus database with same CATH homology


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