3SQ5 | Genus

Total Genus 145

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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	145
sequence length	460
structure length	419
Chain Sequence	GAVFKLMKSDFYEREDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPANSKFYMHCATNSQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLRKVTCRTFTRDPTHVAVPFTLPVIPYDLAEDECFCL

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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

molecule tags	Hydrolase
source organism	Saccharomyces cerevisiae
publication title	Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily. pubmed doi rcsb
molecule keywords	Tyrosyl-DNA phosphodiesterase 1
total genus	145
structure length	419
sequence length	460
chains with identical sequence	B, C, D
ec nomenclature	ec 3.1.4.-:
pdb deposition date	2011-07-04

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	3sq5A01
3.30.870.20	Alpha Beta	2-Layer Sandwich	Endonuclease; Chain A	Phospholipase D/nuclease; domain 2	3sq5A02

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

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

#chains in the Genus database with same CATH superfamily
 1BYR A;  2O8R A;  3SQ3 A;  1RFI A;  1RGU A;  1F0I A;  1V0U A;  4GEN A;  1V0T A;  5BQT A;  1MU9 A;  1Q32 A;  5LZK A;  2C1L A;  3SQ7 A;  4RCT A;  1RG2 A;  2F5T X;  1RFF A;  1V0W A;  1JY1 A;  3SQ8 A;  1NOP A;  2ZE9 A;  3SQ5 A;  1XDO A;  1RGT A;  4GGK A;  4URJ A;  1XDP A;  1BYS A;  3HSI A;  5BOX A;  1MU7 A;  3QPH A;  5BPI A;  4GEM A;  4GGJ A;  1RG1 A;  4GEL A;  1QZQ A;  4H4A A;  1RH0 A;  1V0R A;  2ZE4 A;  1V0V A;  1V0Y A;  1V0S A;  5BPD A; 
#chains in the Genus database with same CATH topology
 1BYR A;  2O8R A;  3SQ3 A;  1RFI A;  1RGU A;  1F0I A;  1V0U A;  1VSR A;  2YMB A;  4GEN A;  1V0T A;  4A5Z A;  3HRL A;  5BQT A;  1MU9 A;  1Q32 A;  3R3P A;  5LZK A;  2C1L A;  3SQ7 A;  4RCT A;  1RG2 A;  2F5T X;  1RFF A;  1V0W A;  1JY1 A;  3SQ8 A;  1NOP A;  2ZE9 A;  3SQ5 A;  1XDO A;  1RGT A;  4GGK A;  4URJ A;  1XDP A;  1BYS A;  3HSI A;  5BOX A;  1MU7 A;  3QPH A;  5BPI A;  4GEM A;  4GGJ A;  1CW0 A;  1RG1 A;  4GEL A;  1QZQ A;  4H4A A;  1RH0 A;  1V0R A;  2ZE4 A;  1V0V A;  1ODG A;  1V0Y A;  1V0S A;  5BPD A; 
#chains in the Genus database with same CATH homology
 1BYR A;  2O8R A;  3SQ3 A;  1RFI A;  1RGU A;  1F0I A;  1V0U A;  4GEN A;  1V0T A;  5BQT A;  1MU9 A;  1Q32 A;  5LZK A;  2C1L A;  3SQ7 A;  4RCT A;  1RG2 A;  2F5T X;  1RFF A;  1V0W A;  1JY1 A;  3SQ8 A;  1NOP A;  2ZE9 A;  3SQ5 A;  1XDO A;  1RGT A;  4GGK A;  4URJ A;  1XDP A;  1BYS A;  3HSI A;  5BOX A;  1MU7 A;  3QPH A;  5BPI A;  4GEM A;  4GGJ A;  1RG1 A;  4GEL A;  1QZQ A;  4H4A A;  1RH0 A;  1V0R A;  2ZE4 A;  1V0V A;  1V0Y A;  1V0S A;  5BPD 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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#similar chains, but unknotted
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3SQ5A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations