3SQ3 | Genus

Total Genus 133

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	133
sequence length	462
structure length	424
Chain Sequence	GAVFKLMKSDFYEREDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHATKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATNSQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDPTHVAVPFTLPVIPYDLAEDECFCLAL

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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	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
molecule tags	Hydrolase
source organism	Saccharomyces cerevisiae
total genus	133
structure length	424
sequence length	462
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	3sq3A01
3.30.870.20	Alpha Beta	2-Layer Sandwich	Endonuclease; Chain A	Phospholipase D/nuclease; domain 2	3sq3A02

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

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

#chains in the Genus database with same CATH superfamily
 1RFF A;  1V0U A;  4GEL A;  1MU9 A;  3SQ7 A;  4URJ A;  1NOP A;  1V0T A;  3HSI A;  2O8R A;  3QPH A;  4H4A A;  4RCT A;  1JY1 A;  1RG2 A;  2C1L A;  1BYR A;  1Q32 A;  3SQ5 A;  1RFI A;  3SQ3 A;  1RGU A;  2F5T X;  5BPI A;  1F0I A;  4GEN A;  5BOX A;  1V0R A;  4GGK A;  1XDO A;  3SQ8 A;  1RGT A;  1V0V A;  1MU7 A;  1RH0 A;  1V0Y A;  5BPD A;  4GEM A;  1V0S A;  5LZK A;  1XDP A;  1RG1 A;  2ZE9 A;  4GGJ A;  5BQT A;  1BYS A;  1QZQ A;  1V0W A;  2ZE4 A; 
#chains in the Genus database with same CATH topology
 1RFF A;  1V0U A;  4GEL A;  1MU9 A;  3SQ7 A;  1ODG A;  4URJ A;  1NOP A;  1V0T A;  3HSI A;  2O8R A;  3QPH A;  4H4A A;  4RCT A;  1JY1 A;  2YMB A;  1RG2 A;  2C1L A;  3R3P A;  1BYR A;  1Q32 A;  3SQ5 A;  1RFI A;  3SQ3 A;  1RGU A;  2F5T X;  5BPI A;  1F0I A;  4GEN A;  5BOX A;  1CW0 A;  1V0R A;  4GGK A;  1XDO A;  3SQ8 A;  1RGT A;  1V0V A;  1MU7 A;  1RH0 A;  1V0Y A;  5BPD A;  4GEM A;  1V0S A;  1VSR A;  5LZK A;  1XDP A;  4A5Z A;  1RG1 A;  2ZE9 A;  4GGJ A;  5BQT A;  1BYS A;  1QZQ A;  3HRL A;  1V0W A;  2ZE4 A; 
#chains in the Genus database with same CATH homology
 1RFF A;  1V0U A;  4GEL A;  1MU9 A;  3SQ7 A;  4URJ A;  1NOP A;  1V0T A;  3HSI A;  2O8R A;  3QPH A;  4H4A A;  4RCT A;  1JY1 A;  1RG2 A;  2C1L A;  1BYR A;  1Q32 A;  3SQ5 A;  1RFI A;  3SQ3 A;  1RGU A;  2F5T X;  5BPI A;  1F0I A;  4GEN A;  5BOX A;  1V0R A;  4GGK A;  1XDO A;  3SQ8 A;  1RGT A;  1V0V A;  1MU7 A;  1RH0 A;  1V0Y A;  5BPD A;  4GEM A;  1V0S A;  5LZK A;  1XDP A;  1RG1 A;  2ZE9 A;  4GGJ A;  5BQT A;  1BYS A;  1QZQ A;  1V0W A;  2ZE4 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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3SQ3A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations