3SQ5A

Crystal structure analysis of the yeast tyrosyl-dna phosphodiesterase h432n mutant
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

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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publication title Analysis of the active-site mechanism of tyrosyl-DNA phosphodiesterase I: a member of the phospholipase D superfamily.
pubmed doi rcsb
molecule tags Hydrolase
source organism Saccharomyces cerevisiae
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
ClassArchitectureTopologyHomologyDomain
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 1RFIA 5BPIA 4URJA 3SQ7A 1RH0A 1V0VA 1BYSA 1MU9A 1RG2A 5LZKA 2F5TX 1MU7A 1V0UA 4GENA 3SQ3A 4GGJA 1QZQA 1NOPA 1XDOA 1V0WA 3HSIA 1XDPA 4RCTA 1V0RA 2ZE4A 5BPDA 5BOXA 5BQTA 1JY1A 1RGTA 1V0TA 1V0YA 1RGUA 1F0IA 3SQ8A 3QPHA 3SQ5A 2O8RA 4GEMA 1RFFA 1RG1A 1V0SA 2ZE9A 4H4AA 2C1LA 1Q32A 4GGKA 4GELA
chains in the Genus database with same CATH superfamily
1BYRA 1RFIA 5BPIA 4URJA 3SQ7A 1RH0A 1V0VA 1BYSA 1MU9A 1RG2A 5LZKA 2F5TX 1MU7A 1V0UA 4GENA 3SQ3A 3HRLA 1QZQA 4GGJA 1NOPA 1XDOA 1V0WA 3HSIA 1XDPA 2YMBA 4RCTA 1V0RA 1ODGA 2ZE4A 4A5ZA 5BPDA 5BOXA 5BQTA 1JY1A 1RGTA 1V0TA 1V0YA 1RGUA 1F0IA 1CW0A 3SQ8A 3QPHA 3SQ5A 3R3PA 2O8RA 4GEMA 1RFFA 1RG1A 1V0SA 1VSRA 2ZE9A 4H4AA 2C1LA 1Q32A 4GGKA 4GELA
chains in the Genus database with same CATH topology
1BYRA 1RFIA 5BPIA 4URJA 3SQ7A 1RH0A 1V0VA 1BYSA 1MU9A 1RG2A 5LZKA 2F5TX 1MU7A 1V0UA 4GENA 3SQ3A 4GGJA 1QZQA 1NOPA 1XDOA 1V0WA 3HSIA 1XDPA 4RCTA 1V0RA 2ZE4A 5BPDA 5BOXA 5BQTA 1JY1A 1RGTA 1V0TA 1V0YA 1RGUA 1F0IA 3SQ8A 3QPHA 3SQ5A 2O8RA 4GEMA 1RFFA 1RG1A 1V0SA 2ZE9A 4H4AA 2C1LA 1Q32A 4GGKA 4GELA
chains in the Genus database with same CATH homology


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