4X5E | 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
sequence length	348
structure length	345
Chain Sequence	VPSWPQILGRLTDNRDLARGQAAWAMDQIMTGNARPAQIAAFAVAMTMKAPTADEVGELAGVMLSHAHPLPADTVPDDAVDVVGTGGDGVNTVNLSTMAAIVVAAAGVPVVKHGNRALSGGADTLEALGVRIDLGPDLVARSLAEVGIGFCFAPRFHPSYRHAAAVRAEIGVPTVFNLLGPLTNPARPRAGLIGCAFADLAEVMAGVFAARRSSVLVVHGDDGLDELTTTTTSTIWRVAAGSVDKLTFDPAGFGFARAQLDQLAGGDAQANAAAVRAVLGGARGPVRDAVVLNAAGAIVAHAGLSSRAEWLPAWEEGLRRASAAIDTGAAEQLLARWVRFGRQIL

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__018565623017875__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__018565623017875__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4X5E/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__018565623017875__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"018565623017875","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4X5E/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__018565623017875__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d00c393127ba3e1f221c592/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d00c393127ba3e1f221c592/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d00c393127ba3e1f221c592/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/5d00c393127ba3e1f221c592/pdb.gz): 569 ms

reading 345 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

345 atoms created

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

Time for creating model: 27 ms

Adding embedded #jmolscript: select ({0:344});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

publication title	Structures of Mycobacterium tuberculosis Anthranilate Phosphoribosyltransferase Variants Reveal the Conformational Changes That Facilitate Delivery of the Substrate to the Active Site. pubmed doi rcsb
molecule keywords	Anthranilate phosphoribosyltransferase
molecule tags	Transferase
source organism	Mycobacterium tuberculosis
total genus	119
structure length	345
sequence length	348
chains with identical sequence	B
ec nomenclature	ec 2.4.2.18: Anthranilate phosphoribosyltransferase.
pdb deposition date	2014-12-05

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00591	Glycos_transf_3	Glycosyl transferase family, a/b domain
A	PF02885	Glycos_trans_3N	Glycosyl transferase family, helical bundle domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.20.970.10	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3	Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C	4x5eA01
3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	4x5eA02

4ZOKA 2ELCA 2J0FA 4X5EA 4GIUA 5BYTA 4GA5A 1ZXYA 4X5BA 4N8QA 5C2LA 3H5QA 5BO3A 4YYYA 2WK5A 2BPQA 4OWOA 1OTPA 4X5AA 4EADA 5BNEA 1ZVWA 4ZTVA 4OWNA 4MUOA 5EY3A 2WK6A 4OWSA 4GTNA 4ZOJA 1ZYKA 4GKMA 4OWQA 4X59A 4IJ1A 4LHMA 4EAFA 1KGZA 4HKMA 3QSAA 2GVQA 4N93A 3R88A 4XR5A 4X5DA 4YI7A 5BO2A 3TWPA 5EP8A 1AZYA 3UU1A 1GXBA 4X5CA 1V8GA 3GBRA 4ZOFA 5C1RA 1O17A 4N5VA 2TPTA 1UOUA 3R6CA 4GA6A 5C7SA 4GA4A 3QS8A 4M0RA 1BRWA 4OWVA 2DSJA 1KHDA 4OWMA 4YEKA 4X58A 3QR9A 4X46A 3QQSA 1VQUA 4OWUA
chains in the Genus database with same CATH superfamily

4ZOKA 2ELCA 2J0FA 4X5EA 4GIUA 4GA5A 5BYTA 1ZXYA 4X5BA 4N8QA 5C2LA 3H5QA 5BO3A 4YYYA 2WK5A 2BPQA 1RF8B 4OWOA 1OTPA 4X5AA 4EADA 5BNEA 1ZVWA 4ZTVA 4OWNA 4MUOA 5EY3A 2WK6A 4OWSA 4GTNA 4ZOJA 1ZYKA 4GKMA 4OWQA 4X59A 4IJ1A 4LHMA 4EAFA 1KGZA 4HKMA 3QSAA 2GVQA 4N93A 3R88A 4XR5A 4X5DA 4YI7A 5BO2A 3TWPA 5EP8A 1AZYA 3UU1A 4F3FC 1GXBA 4X5CA 1V8GA 3GBRA 4ZOFA 5C1RA 1O17A 4N5VA 2TPTA 1UOUA 1RRZA 3R6CA 4GA6A 5C7SA 4GA4A 3QS8A 4M0RA 1BRWA 4OWVA 2DSJA 1KHDA 4OWMA 4YEKA 4X58A 3QR9A 4X46A 3QQSA 1VQUA 4OWUA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 4ZOK A;  2ELC A;  2J0F A;  4X5E A;  4GIU A;  5BYT A;  4GA5 A;  1ZXY A;  4X5B A;  4N8Q A;  5C2L A;  3H5Q A;  5BO3 A;  4YYY A;  2WK5 A;  2BPQ A;  4OWO A;  1OTP A;  4X5A A;  4EAD A;  5BNE A;  1ZVW A;  4ZTV A;  4OWN A;  4MUO A;  5EY3 A;  2WK6 A;  4OWS A;  4GTN A;  4ZOJ A;  1ZYK A;  4GKM A;  4OWQ A;  4X59 A;  4IJ1 A;  4LHM A;  4EAF A;  1KGZ A;  4HKM A;  3QSA A;  2GVQ A;  4N93 A;  3R88 A;  4XR5 A;  4X5D A;  4YI7 A;  5BO2 A;  3TWP A;  5EP8 A;  1AZY A;  3UU1 A;  1GXB A;  4X5C A;  1V8G A;  3GBR A;  4ZOF A;  5C1R A;  1O17 A;  4N5V A;  2TPT A;  1UOU A;  3R6C A;  4GA6 A;  5C7S A;  4GA4 A;  3QS8 A;  4M0R A;  1BRW A;  4OWV A;  2DSJ A;  1KHD A;  4OWM A;  4YEK A;  4X58 A;  3QR9 A;  4X46 A;  3QQS A;  1VQU A;  4OWU A; 
#chains in the Genus database with same CATH topology
 4ZOK A;  2ELC A;  2J0F A;  4X5E A;  4GIU A;  4GA5 A;  5BYT A;  1ZXY A;  4X5B A;  4N8Q A;  5C2L A;  3H5Q A;  5BO3 A;  4YYY A;  2WK5 A;  2BPQ A;  1RF8 B;  4OWO A;  1OTP A;  4X5A A;  4EAD A;  5BNE A;  1ZVW A;  4ZTV A;  4OWN A;  4MUO A;  5EY3 A;  2WK6 A;  4OWS A;  4GTN A;  4ZOJ A;  1ZYK A;  4GKM A;  4OWQ A;  4X59 A;  4IJ1 A;  4LHM A;  4EAF A;  1KGZ A;  4HKM A;  3QSA A;  2GVQ A;  4N93 A;  3R88 A;  4XR5 A;  4X5D A;  4YI7 A;  5BO2 A;  3TWP A;  5EP8 A;  1AZY A;  3UU1 A;  4F3F C;  1GXB A;  4X5C A;  1V8G A;  3GBR A;  4ZOF A;  5C1R A;  1O17 A;  4N5V A;  2TPT A;  1UOU A;  1RRZ A;  3R6C A;  4GA6 A;  5C7S A;  4GA4 A;  3QS8 A;  4M0R A;  1BRW A;  4OWV A;  2DSJ A;  1KHD A;  4OWM A;  4YEK A;  4X58 A;  3QR9 A;  4X46 A;  3QQS A;  1VQU A;  4OWU A; 
#chains in the Genus database with same CATH homology
 4ZOK A;  2ELC A;  2J0F A;  4X5E A;  4GIU A;  5BYT A;  4GA5 A;  1ZXY A;  4X5B A;  4N8Q A;  5C2L A;  3H5Q A;  5BO3 A;  4YYY A;  2WK5 A;  2BPQ A;  4OWO A;  1OTP A;  4X5A A;  4EAD A;  5BNE A;  1ZVW A;  4ZTV A;  4OWN A;  4MUO A;  5EY3 A;  2WK6 A;  4OWS A;  4GTN A;  4ZOJ A;  1ZYK A;  4GKM A;  4OWQ A;  4X59 A;  4IJ1 A;  4LHM A;  4EAF A;  1KGZ A;  4HKM A;  3QSA A;  2GVQ A;  4N93 A;  3R88 A;  4XR5 A;  4X5D A;  4YI7 A;  5BO2 A;  3TWP A;  5EP8 A;  1AZY A;  3UU1 A;  1GXB A;  4X5C A;  1V8G A;  3GBR A;  4ZOF A;  5C1R A;  1O17 A;  4N5V A;  2TPT A;  1UOU A;  3R6C A;  4GA6 A;  5C7S A;  4GA4 A;  3QS8 A;  4M0R A;  1BRW A;  4OWV A;  2DSJ A;  1KHD A;  4OWM A;  4YEK A;  4X58 A;  3QR9 A;  4X46 A;  3QQS A;  1VQU A;  4OWU 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...

4X5EA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations