1Q32 | Genus

Total Genus 144

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	144
sequence length	460
structure length	419
Chain Sequence	GAVFKLMKSDFYEREDMITLKDIFGTETLKRSILFSFQYELDFLLRQFHQNVENITIVGQKGTIMPIEARAMDATLAVILKKVKLIEITMPPFASHHTKLIINFYDNGECKIFLPSNNFTSMETNLPQQVCWCSPLLKIGKEGLPVPFKRSLIEYLNSYHLKDIDELITKSVEEVNFAPLSELEFVYSTPSKFQSSGLLSFYNKLEKLSDTAKHYLCQTSSIGTSLSRARDENLWTHLMIPLFTGIMSPPILPTNSLINEYSQRKIKPYIIFPTEQEFVTSPLKWSSSGWFHFQYLQKKSYYEMLRNKFKVFYKQDPAMVTRRRGTTPAHSKFYMHCATNSQVFKELEWCLYTSANLSQTAWGTVSRKPRNYEAGVLYHSRRLRKVTCRTFTRDPTHVAVPFTLPVIPYDLAEDECFCL

Loading diagram...

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

loadScript /static/js/j2s/core/package.js

loadScript /static/js/j2s/core/corejmol.z.js

loadScript /static/js/j2s/core/corescript.z.js

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__370441720586931__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__370441720586931__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1Q32/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__370441720586931__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"370441720586931","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1Q32/A/"

Jmol Version: 14.29.13 2018-04-17 17:17

java.vendor: Java2Script (HTML5)

java.version: 2018-01-28 23:38:52 (JSmol/j2s)

os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)

Access: ALL

memory: 0.0/0.0

processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor white

backgroundColor = "white"

Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

Jmol getValue ATOMMOVEDCallback null

Jmol getValue AUDIOCallback null

Jmol getValue CLICKCallback null

Jmol getValue DRAGDROPCallback null

Jmol getValue ECHOCallback null

Jmol getValue ERRORCallback null

Jmol getValue EVALCallback null

Jmol getValue HOVERCallback null

Jmol getValue IMAGECallback null

Jmol getValue LOADSTRUCTCallback null

Jmol getValue MEASURECallback null

Jmol getValue MESSAGECallback null

Jmol getValue MINIMIZATIONCallback null

Jmol getValue SERVICECallback null

Jmol getValue PICKCallback null

Jmol getValue RESIZECallback null

Jmol getValue SCRIPTCallback null

Jmol getValue SYNCCallback null

Jmol getValue STRUCTUREMODIFIEDCallback null

Jmol getValue doTranslate null

language=en_US

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__370441720586931__ ready

script 1 started

platformSpeed = 8

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	Mutation of a conserved active site residue converts tyrosyl-DNA phosphodiesterase I into a DNA topoisomerase I-dependent poison pubmed doi rcsb
molecule keywords	tyrosyl-DNA phosphodiesterase
molecule tags	Replication,transcription,hydrolase
source organism	Saccharomyces cerevisiae
total genus	144
structure length	419
sequence length	460
chains with identical sequence	B, C, D
ec nomenclature	ec 3.1.4.-:
pdb deposition date	2003-07-28

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	1q32A01
3.30.870.20	Alpha Beta	2-Layer Sandwich	Endonuclease; Chain A	Phospholipase D/nuclease; domain 2	1q32A02

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

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

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

...loading similar chains, please wait...
similar chains in the Genus database (?% sequence similarity)

...loading similar chains, please wait...
similar chains in the pdb database (?% sequence similarity)

#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...

1Q32A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations