3SQ5 | Genus

Total Genus 145

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

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	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

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

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations