3TW5 | Genus

Total Genus 91

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	91
sequence length	366
structure length	344
Chain Sequence	EANGNQDIAKLEAYFGTKMEMTLKDLPTVGVHTPSPWAGPYWPTYQDSINVQWSQGQPSAAEKYAKAFGKDVKTFMDAVSKKNGIDSQSGRKKCSSDDDCSTLTDGSSCSIRTGKTSGYCIPTWFGISHAWSPAAILETEPKCPVKHNGVTFQPMDLKALVSLVYDGARVQTVFTGDLNPAYFHIASANILGKLNSTFVADVTAGAEVWNQPVRGFKVYEQTEMTLEEGAQTFYGLEAYPWNAAAKSLVYVKSRLSWIYETYTDGGLVSSGQIDKFTTGQYYYYLLELDDAGEIIGGEWVYGSDDDHPDFLWLPKAKPAANTVTSVGLSYADVSMLLKKSAACT

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__3269099553136505__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__3269099553136505__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3TW5/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__3269099553136505__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"3269099553136505","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3TW5/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__3269099553136505__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0320f982f5e466974b9336/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0320f982f5e466974b9336/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d0320f982f5e466974b9336/pdb.gz)

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

The Resolver thinks Pdb

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

Time for openFile(/file/5d0320f982f5e466974b9336/pdb.gz): 616 ms

reading 344 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

344 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:343});backbone only;select *;

platformSpeed = 8

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

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

specularPower = 9

ambientPercent = 20

antialiasDisplay = true

Script completed

Jmol script terminated

loadScript /static/js/j2s/J/g3d/HermiteRenderer.js

loadScript /static/js/j2s/J/renderbio/BioMeshRenderer.js

loadScript /static/js/j2s/J/render/MeshRenderer.js

loadScript /static/js/j2s/J/shape/Mesh.js

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

molecule tags	Transferase
source organism	Phytophthora sojae
publication title	Structural and Phylogenetic Analyses of the GP42 Transglutaminase from Phytophthora sojae Reveal an Evolutionary Relationship between Oomycetes and Marine Vibrio Bacteria. pubmed doi rcsb
molecule keywords	Transglutaminase elicitor
total genus	91
structure length	344
sequence length	366
chains with identical sequence	B
ec nomenclature	ec 2.3.2.13: Protein-glutamine gamma-glutamyltransferase.
pdb deposition date	2011-09-21

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF16683	TGase_elicitor	Transglutaminase elicitor

Image from the rcsb pdb (www.rcsb.org)

cath code	Class	Architecture	Topology	Homology	Domain
1.10.220.130	Mainly Alpha	Orthogonal Bundle	Annexin V; domain 1	Annexin V; domain 1	3tw5A02

3TW5A
chains in the Genus database with same CATH superfamily

1AVCA 1R8ME 1BC0A 4FHRB 1BO9A 4Q2SA 4KN7X 3ANYA 2OY9A 1N44A 3AO0A 1ANWA 3ABSA 1HVGA 1YIIA 2R0DA 2H0LA 2ZHJA 1N41A 1YCNA 4C0AA 1DK5A 1W7BA 3L8NA 2HYVA 1BC3A 4EVHA 1R8SE 2QEZA 2HYWA 2RANA 1LKVX 1R8QE 1M9IA 1AOWA 4JMIA 1BCWA 2XO2A 3ABOA 4OIYA 1PBVA 1ANNA 1AXNA 1HVDA 2IICA 1AEIA 4D7QA 1MCXA 3HJLA 1XJLA 3USWA 3SOHB 2HSNA 3BRXA 1W3WA 1XT0B 4JK1X 4HREA 1G5NA 2R09A 1UPTB 3ABRA 1N00A 1RE0B 1C1KA 4L5MA 1DM5A 3AJCA 4A4PA 2HYUA 1HVEA 1YJ0A 1Q8DA 2IE7A 2ZOCA 4MDVA 2H0KA 4KMUX 2VXGA 4D7RA 1BC1A 2K6XA 1HM6A 2IE6A 1QC7A 4X9PA 1BCYA 1R4AE 4JXHA 3USYA 2XO3A 3SWVA 4KN4X 4Z21A 1AVHA 1A8AA 1I4AA 4JWLA 1HVFA 4EVFA 2ZHIA 1A8BA 1N42A 4C7PA 3ABQA 1S9DE 4JMOA 1SAVA 1W45A 4MDUA 1AIIA 3LTLA 1HAKA 2II2A 1ANXA 1YGMA 1ALAA 1XSZA 1KU1A 4FQ0C 1BC9A 2H0MA 1BCZA 3TW5A 1AVRA 2Q4CA
chains in the Genus database with same CATH topology

1R8ME 1R8SE 4C7PA 1LKVX 4A4PA 1R8QE 1S9DE 4FHRB 4JMOA 1Q8DA 4JMIA 4KMUX 4OIYA 4KN7X 4D7RA 2K6XA 1PBVA 4L5MA 1QC7A 3LTLA 3HJLA 1XSZA 2R0DA 4JXHA 3USYA 1KU1A 3USWA 3SOHB 3SWVA 2HSNA 4FQ0C 4KN4X 4Z21A 1BC9A 1XT0B 4JK1X 2R09A 3TW5A 4JWLA 4C0AA 3L8NA 1RE0B 4D7QA 3AJCA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3TW5 A; 
#chains in the Genus database with same CATH topology
 1AVC A;  1R8M E;  1BC0 A;  4FHR B;  1BO9 A;  4Q2S A;  4KN7 X;  3ANY A;  2OY9 A;  1N44 A;  3AO0 A;  1ANW A;  3ABS A;  1HVG A;  1YII A;  2R0D A;  2H0L A;  2ZHJ A;  1N41 A;  1YCN A;  4C0A A;  1DK5 A;  1W7B A;  3L8N A;  2HYV A;  1BC3 A;  4EVH A;  1R8S E;  2QEZ A;  2HYW A;  2RAN A;  1LKV X;  1R8Q E;  1M9I A;  1AOW A;  4JMI A;  1BCW A;  2XO2 A;  3ABO A;  4OIY A;  1PBV A;  1ANN A;  1AXN A;  1HVD A;  2IIC A;  1AEI A;  4D7Q A;  1MCX A;  3HJL A;  1XJL A;  3USW A;  3SOH B;  2HSN A;  3BRX A;  1W3W A;  1XT0 B;  4JK1 X;  4HRE A;  1G5N A;  2R09 A;  1UPT B;  3ABR A;  1N00 A;  1RE0 B;  1C1K A;  4L5M A;  1DM5 A;  3AJC A;  4A4P A;  2HYU A;  1HVE A;  1YJ0 A;  1Q8D A;  2IE7 A;  2ZOC A;  4MDV A;  2H0K A;  4KMU X;  2VXG A;  4D7R A;  1BC1 A;  2K6X A;  1HM6 A;  2IE6 A;  1QC7 A;  4X9P A;  1BCY A;  1R4A E;  4JXH A;  3USY A;  2XO3 A;  3SWV A;  4KN4 X;  4Z21 A;  1AVH A;  1A8A A;  1I4A A;  4JWL A;  1HVF A;  4EVF A;  2ZHI A;  1A8B A;  1N42 A;  4C7P A;  3ABQ A;  1S9D E;  4JMO A;  1SAV A;  1W45 A;  4MDU A;  1AII A;  3LTL A;  1HAK A;  2II2 A;  1ANX A;  1YGM A;  1ALA A;  1XSZ A;  1KU1 A;  4FQ0 C;  1BC9 A;  2H0M A;  1BCZ A;  3TW5 A;  1AVR A;  2Q4C A; 
#chains in the Genus database with same CATH homology
 1R8M E;  1R8S E;  4C7P A;  1LKV X;  4A4P A;  1R8Q E;  1S9D E;  4FHR B;  4JMO A;  1Q8D A;  4JMI A;  4KMU X;  4OIY A;  4KN7 X;  4D7R A;  2K6X A;  1PBV A;  4L5M A;  1QC7 A;  3LTL A;  3HJL A;  1XSZ A;  2R0D A;  4JXH A;  3USY A;  1KU1 A;  3USW A;  3SOH B;  3SWV A;  2HSN A;  4FQ0 C;  4KN4 X;  4Z21 A;  1BC9 A;  1XT0 B;  4JK1 X;  2R09 A;  3TW5 A;  4JWL A;  4C0A A;  3L8N A;  1RE0 B;  4D7Q A;  3AJC 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...

3TW5A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations