4DZ4 | Genus

Total Genus 119

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	119
Knots found	KnotProt 2.0: S +3₁
sequence length	316
structure length	313
Chain Sequence	TLYGDGAIRRPSVYGSSIENTYAGVLSFMRRNYTRDLDGVDVVVSGVPLDLATTFRSGARLGPSAVRAASVQLAELNPYPWGFDPFDDLAVIDYGDCWFDAHHPLSIKPAIVEHARTILQSDARMLTLGGDHYITYPLLIAHAQKYGKPLSLIHFDAHCDTWADDSLNHGTMFYKAVKDGLIDPKASVQVGIRTWNDDYLGINVLDAAWVHEHGARATLERIESIVGGRPAYLTFDIDCLDPAFAPGTGTPVAGGLSSAQALAIVRGLGGVNLIGADVVEVAPAYDQSEITAIAAAHVACDLLCLWRQRKAGA

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__825765914138722__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__825765914138722__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4DZ4/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__825765914138722__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"825765914138722","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4DZ4/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__825765914138722__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d03b2fe16b0e5dbb8aae971/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d03b2fe16b0e5dbb8aae971/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d03b2fe16b0e5dbb8aae971/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/5d03b2fe16b0e5dbb8aae971/pdb.gz): 532 ms

reading 313 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

313 atoms created

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

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:312});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	Hydrolase
source organism	Burkholderia thailandensis
publication title	Combining functional and structural genomics to sample the essential Burkholderia structome. pubmed doi rcsb
molecule keywords	Agmatinase
total genus	119
structure length	313
sequence length	316
chains with identical sequence	B, C, D, E, F
other databases	KnotProt 2.0: S +3₁
ec nomenclature	ec 3.5.3.11: Agmatinase.
pdb deposition date	2012-02-29

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00491	Arginase	Arginase family

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

cath code	Class	Architecture	Topology	Homology	Domain
3.40.800.10	Alpha Beta	3-Layer(aba) Sandwich	Arginase; Chain A	Ureohydrolase domain	4dz4A00

4FCIA 3THJA 2EF5A 3CEVA 4HZEA 4Q3RC 4IXUA 3SJTA 1P8OA 4RHJA 2EIVA 1R1OA 1HQGA 4Q3UA 4IE3A 1CEVA 1PQ3A 4RHKA 2A0MA 2EF4A 4I06A 4IU5A 3GN0A 3E6KA 5RLAA 3NIOA 5HJ9A 1ZPGA 4MYKA 1ZPEA 2PHAA 3MJLA 4IU1A 1TBLA 3M1RA 3E9BA 4HWWA 4MYFA 4FCKA 4IE1A 1P8SA 2PLLA 4Q3TA 4DZ4A 4Q3PA 1P8MA 3LHLA 1WOIA 4RHMA 4IU4A 1T4PA 3PZLA 4CEVA 4Q42A 4Q3QA 2AEBA 1D3VA 1T4SA 4RHQA 4GSVA 3E6VA 3THHA 4Q40A 1WVAA 3SL1A 1WVBA 3MFVA 4RHLA 4G3HA 1HQXA 1T4TA 1T5GA 1GQ6A 3LP4A 4RHIA 3SKKA 4IE2A 1WOGA 2ZAVA 4GSMA 1T4RA 4GSZA 4Q3VA 4MXRA 3THEA 4MYNA 4MYLA 5CEVA 5HJAA 3TF3A 1WOHA 1P8PA 3RLAA 1RLAA 4Q41A 1HQFA 3E8QA 3DJ8A 4IXVA 3MFWA 2PHOA 4Q3SA 3GMZA 3SL0A 3MMRA 2CEVA 4Q3RA 2RLAA 3E8ZA 3KV2A 1TA1A 3NIPA 3NIQA 1P8QA 4RLAA 1P8RA 3F80A 1GQ7A 4IU0A 4ITYA 4GWDA 1HQ5A 1T5FA 1P8NA 4GWCA 1TBHA 3LP7A 1HQHA 1TBJA 4HXQA 1XFKA 3TH7A
chains in the Genus database with same CATH superfamily

4FCIA 3THJA 1C3RA 3MENA 2EF5A 3CEVA 4HZEA 4Q3RC 4IXUA 3RQDA 1P8OA 4RHJA 3SJTA 4CBTA 2EIVA 1R1OA 1HQGA 4Q3UA 4IE3A 3F0RA 2VQMA 5EFKB 5THUA 1CEVA 1PQ3A 4RHKA 2A0MA 2EF4A 4I06A 4IU5A 5G10A 3GN0A 3E6KA 5RLAA 3EZPA 3NIOA 5HJ9A 3MZ3A 1ZPGA 4MYKA 4RN1A 1ZPEA 5G0GA 2PHAA 4BZ7A 3SFFA 3EW8A 3MJLA 4ZURA 3SFHA 4IU1A 5ICNB 5G0IA 2V5WA 1T64A 1TBLA 3M1RA 3E9BA 3F06A 4HWWA 4MYFA 5D1CA 4FCKA 4IE1A 5EEMA 3C0ZA 1P8SA 2PLLA 5EFNA 4RN0A 4Q3TA 3ZNSA 4DZ4A 4Q3PA 4QA6A 1P8MA 2VQQA 3LHLA 1WOIA 4RHMA 4IU4A 1T4PA 3Q9EA 3PZLA 5G11A 1C3PA 5DC8A 5EF7A 4Q42A 4QA4A 4CEVA 5LI3A 4Q3QA 5FCWA 2AEBA 1D3VA 1T4SA 4RHQA 5EFHA 4QA5A 4GSVA 5D1DA 5FUEA 5G0YA 3E6VA 3THHA 4Q40A 5DC5A 4QA7A 5EFJD 4CQFA 5EFGA 1WVAA 3Q9FA 3SL1A 1WVBA 3MFVA 4RHLA 5G3WA 4G3HA 4BKXB 1HQXA 5THTA 1T4TA 1T5GA 2VQJA 1GQ6A 4BZ9A 4RN2A 3LP4A 4ZUMA 4BZ8A 3C0YA 4RHIA 4QA3A 4QA1A 4IE2A 4ZUOA 3SKKA 1WOGA 2ZAVA 4GSMA 1T4RA 4GSZA 2VQWG 5G0HA 4Q3VA 3ZNRA 1W22A 4MXRA 3THEA 3EWFA 4MYNA 4MYLA 5CEVA 5HJAA 3TF3A 1WOHA 1P8PA 3RLAA 1RLAA 1T69A 2VCGA 4A69A 4Q41A 1HQFA 3E8QA 4CBYA 3DJ8A 4IXVA 3MFWA 1C3SA 1T67A 5EEFA 5THSA 3MZ6A 5G1AA 2PHOA 4Q3SA 5G1BA 3GMZA 4BZ6A 3SL0A 3F07A 3MMRA 5A2SA 5EEIA 1ZZ1A 4ZUNA 2CEVA 5THVA 3MZ4A 4LY1A 4Q3RA 5EENA 5DC6A 4BZ5A 2RLAA 3E8ZA 5G0JA 4ZUPA 5EEKA 3KV2A 1ZZ0A 5IX0A 3MZ7A 5G17A 1TA1A 4ZUQA 3NIPA 3NIQA 1P8QA 4RLAA 1P8RA 3F80A 4QA2A 5G13A 1GQ7A 5D1BA 4IU0A 4QA0A 4ITYA 3Q9BA 5G12A 4GWDA 5G1CA 1HQ5A 3MAXA 5EFBD 5BWZA 1T5FA 3EZTA 1VKGA 2VQOA 3C10A 5DC7A 5EF8A 1P8NA 4GWCA 5G0XA 1TBHA 3LP7A 1HQHA 1ZZ3A 2GH6A 4LXZA 1TBJA 2V5XA 5IWGA 4HXQA 1XFKA 3TH7A 2VQVA 3Q9CA 5JI5A
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4FCI A;  3THJ A;  2EF5 A;  3CEV A;  4HZE A;  4Q3R C;  4IXU A;  3SJT A;  1P8O A;  4RHJ A;  2EIV A;  1R1O A;  1HQG A;  4Q3U A;  4IE3 A;  1CEV A;  1PQ3 A;  4RHK A;  2A0M A;  2EF4 A;  4I06 A;  4IU5 A;  3GN0 A;  3E6K A;  5RLA A;  3NIO A;  5HJ9 A;  1ZPG A;  4MYK A;  1ZPE A;  2PHA A;  3MJL A;  4IU1 A;  1TBL A;  3M1R A;  3E9B A;  4HWW A;  4MYF A;  4FCK A;  4IE1 A;  1P8S A;  2PLL A;  4Q3T A;  4DZ4 A;  4Q3P A;  1P8M A;  3LHL A;  1WOI A;  4RHM A;  4IU4 A;  1T4P A;  3PZL A;  4CEV A;  4Q42 A;  4Q3Q A;  2AEB A;  1D3V A;  1T4S A;  4RHQ A;  4GSV A;  3E6V A;  3THH A;  4Q40 A;  1WVA A;  3SL1 A;  1WVB A;  3MFV A;  4RHL A;  4G3H A;  1HQX A;  1T4T A;  1T5G A;  1GQ6 A;  3LP4 A;  4RHI A;  3SKK A;  4IE2 A;  1WOG A;  2ZAV A;  4GSM A;  1T4R A;  4GSZ A;  4Q3V A;  4MXR A;  3THE A;  4MYN A;  4MYL A;  5CEV A;  5HJA A;  3TF3 A;  1WOH A;  1P8P A;  3RLA A;  1RLA A;  4Q41 A;  1HQF A;  3E8Q A;  3DJ8 A;  4IXV A;  3MFW A;  2PHO A;  4Q3S A;  3GMZ A;  3SL0 A;  3MMR A;  2CEV A;  4Q3R A;  2RLA A;  3E8Z A;  3KV2 A;  1TA1 A;  3NIP A;  3NIQ A;  1P8Q A;  4RLA A;  1P8R A;  3F80 A;  1GQ7 A;  4IU0 A;  4ITY A;  4GWD A;  1HQ5 A;  1T5F A;  1P8N A;  4GWC A;  1TBH A;  3LP7 A;  1HQH A;  1TBJ A;  4HXQ A;  1XFK A;  3TH7 A; 
#chains in the Genus database with same CATH topology
 4FCI A;  3THJ A;  1C3R A;  3MEN A;  2EF5 A;  3CEV A;  4HZE A;  4Q3R C;  4IXU A;  3RQD A;  1P8O A;  4RHJ A;  3SJT A;  4CBT A;  2EIV A;  1R1O A;  1HQG A;  4Q3U A;  4IE3 A;  3F0R A;  2VQM A;  5EFK B;  5THU A;  1CEV A;  1PQ3 A;  4RHK A;  2A0M A;  2EF4 A;  4I06 A;  4IU5 A;  5G10 A;  3GN0 A;  3E6K A;  5RLA A;  3EZP A;  3NIO A;  5HJ9 A;  3MZ3 A;  1ZPG A;  4MYK A;  4RN1 A;  1ZPE A;  5G0G A;  2PHA A;  4BZ7 A;  3SFF A;  3EW8 A;  3MJL A;  4ZUR A;  3SFH A;  4IU1 A;  5ICN B;  5G0I A;  2V5W A;  1T64 A;  1TBL A;  3M1R A;  3E9B A;  3F06 A;  4HWW A;  4MYF A;  5D1C A;  4FCK A;  4IE1 A;  5EEM A;  3C0Z A;  1P8S A;  2PLL A;  5EFN A;  4RN0 A;  4Q3T A;  3ZNS A;  4DZ4 A;  4Q3P A;  4QA6 A;  1P8M A;  2VQQ A;  3LHL A;  1WOI A;  4RHM A;  4IU4 A;  1T4P A;  3Q9E A;  3PZL A;  5G11 A;  1C3P A;  5DC8 A;  5EF7 A;  4Q42 A;  4QA4 A;  4CEV A;  5LI3 A;  4Q3Q A;  5FCW A;  2AEB A;  1D3V A;  1T4S A;  4RHQ A;  5EFH A;  4QA5 A;  4GSV A;  5D1D A;  5FUE A;  5G0Y A;  3E6V A;  3THH A;  4Q40 A;  5DC5 A;  4QA7 A;  5EFJ D;  4CQF A;  5EFG A;  1WVA A;  3Q9F A;  3SL1 A;  1WVB A;  3MFV A;  4RHL A;  5G3W A;  4G3H A;  4BKX B;  1HQX A;  5THT A;  1T4T A;  1T5G A;  2VQJ A;  1GQ6 A;  4BZ9 A;  4RN2 A;  3LP4 A;  4ZUM A;  4BZ8 A;  3C0Y A;  4RHI A;  4QA3 A;  4QA1 A;  4IE2 A;  4ZUO A;  3SKK A;  1WOG A;  2ZAV A;  4GSM A;  1T4R A;  4GSZ A;  2VQW G;  5G0H A;  4Q3V A;  3ZNR A;  1W22 A;  4MXR A;  3THE A;  3EWF A;  4MYN A;  4MYL A;  5CEV A;  5HJA A;  3TF3 A;  1WOH A;  1P8P A;  3RLA A;  1RLA A;  1T69 A;  2VCG A;  4A69 A;  4Q41 A;  1HQF A;  3E8Q A;  4CBY A;  3DJ8 A;  4IXV A;  3MFW A;  1C3S A;  1T67 A;  5EEF A;  5THS A;  3MZ6 A;  5G1A A;  2PHO A;  4Q3S A;  5G1B A;  3GMZ A;  4BZ6 A;  3SL0 A;  3F07 A;  3MMR A;  5A2S A;  5EEI A;  1ZZ1 A;  4ZUN A;  2CEV A;  5THV A;  3MZ4 A;  4LY1 A;  4Q3R A;  5EEN A;  5DC6 A;  4BZ5 A;  2RLA A;  3E8Z A;  5G0J A;  4ZUP A;  5EEK A;  3KV2 A;  1ZZ0 A;  5IX0 A;  3MZ7 A;  5G17 A;  1TA1 A;  4ZUQ A;  3NIP A;  3NIQ A;  1P8Q A;  4RLA A;  1P8R A;  3F80 A;  4QA2 A;  5G13 A;  1GQ7 A;  5D1B A;  4IU0 A;  4QA0 A;  4ITY A;  3Q9B A;  5G12 A;  4GWD A;  5G1C A;  1HQ5 A;  3MAX A;  5EFB D;  5BWZ A;  1T5F A;  3EZT A;  1VKG A;  2VQO A;  3C10 A;  5DC7 A;  5EF8 A;  1P8N A;  4GWC A;  5G0X A;  1TBH A;  3LP7 A;  1HQH A;  1ZZ3 A;  2GH6 A;  4LXZ A;  1TBJ A;  2V5X A;  5IWG A;  4HXQ A;  1XFK A;  3TH7 A;  2VQV A;  3Q9C A;  5JI5 A; 
#chains in the Genus database with same CATH homology
 4FCI A;  3THJ A;  2EF5 A;  3CEV A;  4HZE A;  4Q3R C;  4IXU A;  3SJT A;  1P8O A;  4RHJ A;  2EIV A;  1R1O A;  1HQG A;  4Q3U A;  4IE3 A;  1CEV A;  1PQ3 A;  4RHK A;  2A0M A;  2EF4 A;  4I06 A;  4IU5 A;  3GN0 A;  3E6K A;  5RLA A;  3NIO A;  5HJ9 A;  1ZPG A;  4MYK A;  1ZPE A;  2PHA A;  3MJL A;  4IU1 A;  1TBL A;  3M1R A;  3E9B A;  4HWW A;  4MYF A;  4FCK A;  4IE1 A;  1P8S A;  2PLL A;  4Q3T A;  4DZ4 A;  4Q3P A;  1P8M A;  3LHL A;  1WOI A;  4RHM A;  4IU4 A;  1T4P A;  3PZL A;  4CEV A;  4Q42 A;  4Q3Q A;  2AEB A;  1D3V A;  1T4S A;  4RHQ A;  4GSV A;  3E6V A;  3THH A;  4Q40 A;  1WVA A;  3SL1 A;  1WVB A;  3MFV A;  4RHL A;  4G3H A;  1HQX A;  1T4T A;  1T5G A;  1GQ6 A;  3LP4 A;  4RHI A;  3SKK A;  4IE2 A;  1WOG A;  2ZAV A;  4GSM A;  1T4R A;  4GSZ A;  4Q3V A;  4MXR A;  3THE A;  4MYN A;  4MYL A;  5CEV A;  5HJA A;  3TF3 A;  1WOH A;  1P8P A;  3RLA A;  1RLA A;  4Q41 A;  1HQF A;  3E8Q A;  3DJ8 A;  4IXV A;  3MFW A;  2PHO A;  4Q3S A;  3GMZ A;  3SL0 A;  3MMR A;  2CEV A;  4Q3R A;  2RLA A;  3E8Z A;  3KV2 A;  1TA1 A;  3NIP A;  3NIQ A;  1P8Q A;  4RLA A;  1P8R A;  3F80 A;  1GQ7 A;  4IU0 A;  4ITY A;  4GWD A;  1HQ5 A;  1T5F A;  1P8N A;  4GWC A;  1TBH A;  3LP7 A;  1HQH A;  1TBJ A;  4HXQ A;  1XFK A;  3TH7 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...

4DZ4A

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations