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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molecule tags Hydrolase/dna
molecule keywords 5'-D(*AP*GP*AP*GP*TP*T)-3'
publication title Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide
pubmed doi rcsb
source organism Homo sapiens
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
1V0TA 2O8RA 4GEMA 1RH0A 4H4AA 5BOXA 1NOPA 1BYRA 1RG2A 5BPDA 2F5TX 4RCTA 2C1LA 4GGKA 2ZE9A 1RG1A 1MU9A 3QPHA 1Q32A 1JY1A 5BPIA 1QZQA 3SQ3A 1V0SA 1V0YA 4GGJA 3SQ7A 2ZE4A 1V0RA 5BQTA 4URJA 1F0IA 4GELA 1XDPA 1V0WA 1XDOA 1V0VA 1BYSA 3HSIA 1RFFA 4GENA 3SQ8A 1MU7A 1RFIA 1RGTA 1V0UA 5LZKA 3SQ5A 1RGUA
chains in the Genus database with same CATH superfamily
1V0TA 2O8RA 4GEMA 1RH0A 4H4AA 5BOXA 4A5ZA 1NOPA 1BYRA 1RG2A 5BPDA 2F5TX 4RCTA 2C1LA 3R3PA 4GGKA 2ZE9A 1RG1A 1MU9A 3QPHA 1Q32A 1JY1A 5BPIA 1QZQA 3SQ3A 1V0SA 1V0YA 4GGJA 3SQ7A 2ZE4A 1V0RA 5BQTA 4URJA 3HRLA 1F0IA 4GELA 1XDPA 1V0WA 1XDOA 1V0VA 1BYSA 3HSIA 1RFFA 4GENA 3SQ8A 1MU7A 1RFIA 1RGTA 1CW0A 2YMBA 1VSRA 1V0UA 5LZKA 1ODGA 3SQ5A 1RGUA
chains in the Genus database with same CATH topology
1V0TA 2O8RA 4GEMA 1RH0A 4H4AA 5BOXA 1NOPA 1BYRA 1RG2A 5BPDA 2F5TX 4RCTA 2C1LA 4GGKA 2ZE9A 1RG1A 1MU9A 3QPHA 1Q32A 1JY1A 5BPIA 1QZQA 3SQ3A 1V0SA 1V0YA 4GGJA 3SQ7A 2ZE4A 1V0RA 5BQTA 4URJA 1F0IA 4GELA 1XDPA 1V0WA 1XDOA 1V0VA 1BYSA 3HSIA 1RFFA 4GENA 3SQ8A 1MU7A 1RFIA 1RGTA 1V0UA 5LZKA 3SQ5A 1RGUA
chains in the Genus database with same CATH homology


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

 
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