3SQ7A

Crystal structure analysis of the yeast tyrosyl-dna phosphodiesterase h432n_glu mutant
Total Genus 147
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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
147
sequence length
465
structure length
432
Chain Sequence
GAVFKLMKSDFYEREDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSAGTSASDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPANSKFYMHCATSQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLANTRKVTCRTFTRDPTHVAVPFTLPVIPYDLAEDECFCLALEHH
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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 147
structure length 432
sequence length 465
chains with identical sequence B, C, D
ec nomenclature ec 3.1.4.-:
pdb deposition date 2011-07-05

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 3sq7A01
3.30.870.20 Alpha Beta 2-Layer Sandwich Endonuclease; Chain A Phospholipase D/nuclease; domain 2 3sq7A02
1RFFA 3SQ7A 3QPHA 3SQ5A 4GGKA 1RGUA 1BYSA 1NOPA 1JY1A 1V0YA 2O8RA 1F0IA 3SQ3A 3HSIA 5BOXA 4H4AA 1MU9A 1RGTA 4URJA 1V0WA 1V0RA 1MU7A 1RH0A 4GELA 1XDOA 5BPDA 4GEMA 3SQ8A 2F5TX 1RG2A 4GGJA 1V0SA 1V0VA 1V0UA 5BQTA 1Q32A 1V0TA 1QZQA 4RCTA 1RFIA 1RG1A 5LZKA 1XDPA 5BPIA 4GENA 2ZE9A 1BYRA 2ZE4A 2C1LA
chains in the Genus database with same CATH superfamily
1RFFA 3SQ7A 3QPHA 3SQ5A 4GGKA 1RGUA 1ODGA 1BYSA 2YMBA 1NOPA 3R3PA 1JY1A 1V0YA 2O8RA 1F0IA 3SQ3A 3HSIA 5BOXA 4H4AA 1MU9A 1RGTA 4A5ZA 4URJA 1CW0A 1V0WA 1V0RA 1MU7A 3HRLA 1RH0A 4GELA 1XDOA 5BPDA 4GEMA 1VSRA 2F5TX 3SQ8A 1RG2A 4GGJA 1V0SA 1V0VA 1V0UA 5BQTA 1Q32A 1V0TA 1QZQA 4RCTA 1RFIA 1RG1A 5LZKA 1XDPA 5BPIA 4GENA 2ZE9A 1BYRA 2ZE4A 2C1LA
chains in the Genus database with same CATH topology
1RFFA 3SQ7A 3QPHA 3SQ5A 4GGKA 1RGUA 1BYSA 1NOPA 1JY1A 1V0YA 2O8RA 1F0IA 3SQ3A 3HSIA 5BOXA 4H4AA 1MU9A 1RGTA 4URJA 1V0WA 1V0RA 1MU7A 1RH0A 4GELA 1XDOA 5BPDA 4GEMA 3SQ8A 2F5TX 1RG2A 4GGJA 1V0SA 1V0VA 1V0UA 5BQTA 1Q32A 1V0TA 1QZQA 4RCTA 1RFIA 1RG1A 5LZKA 1XDPA 5BPIA 4GENA 2ZE9A 1BYRA 2ZE4A 2C1LA
chains in the Genus database with same CATH homology


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