1RFF | Genus

Total Genus 142

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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	142
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

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After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

publication title	Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes. pubmed doi rcsb
molecule keywords	5'-D(APGPTPT)-3'
molecule tags	Hydrolase/dna
source organism	Homo sapiens
total genus	142
structure length	425
sequence length	447
chains with identical sequence	B
ec nomenclature	ec 3.1.4.-:
pdb deposition date	2003-11-08

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	Class	Architecture	Topology	Homology	Domain
3.30.870.10	Alpha Beta	2-Layer Sandwich	Endonuclease; Chain A	Endonuclease Chain A	1rffA01
3.30.870.20	Alpha Beta	2-Layer Sandwich	Endonuclease; Chain A	Phospholipase D/nuclease; domain 2	1rffA02

2C1LA 4GELA 1RG1A 3QPHA 2ZE9A 1XDPA 1MU9A 1XDOA 4RCTA 3SQ7A 1V0RA 3SQ8A 1NOPA 4GGJA 2F5TX 1RGTA 1MU7A 1F0IA 1RH0A 1V0SA 1BYRA 5BPIA 2ZE4A 5LZKA 1RFIA 1RGUA 1QZQA 4GEMA 1BYSA 4URJA 1V0TA 4GENA 1V0VA 4GGKA 4H4AA 5BQTA 1RFFA 1V0WA 1V0YA 2O8RA 3HSIA 3SQ5A 1RG2A 1V0UA 1Q32A 1JY1A 5BPDA 5BOXA 3SQ3A
chains in the Genus database with same CATH superfamily

2C1LA 4GELA 1RG1A 3QPHA 2ZE9A 1XDPA 1MU9A 1ODGA 1XDOA 4RCTA 3SQ7A 1V0RA 3SQ8A 1NOPA 4GGJA 2F5TX 1RGTA 1MU7A 1F0IA 1RH0A 1V0SA 3HRLA 1BYRA 1CW0A 1VSRA 5BPIA 2ZE4A 5LZKA 1RFIA 1RGUA 1QZQA 4GEMA 1BYSA 4URJA 1V0TA 4GENA 1V0VA 4GGKA 4H4AA 5BQTA 1RFFA 1V0WA 1V0YA 2O8RA 3HSIA 3R3PA 3SQ5A 1RG2A 1V0UA 1Q32A 1JY1A 2YMBA 4A5ZA 5BPDA 5BOXA 3SQ3A
chains in the Genus database with same CATH topology

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

#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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#similar chains in the pdb database (?% sequence similarity)
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1RFFA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations