2QIE | Genus

Total Genus 40

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	40
sequence length	136
structure length	136
Chain Sequence	MKQFEIVIEPIQTEQYREFTINEYQGAVVVFTGHVREWTKGVKTEYLEYEAYIPMAEKKLAQIGDEINEKWPGTITSIVHRIGPLQISDIAVLIAVSSPHRKDAYRANEYAIERIKEIVPIWKKEIWEDGSKWQGH

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__303868261998302__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__303868261998302__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2QIE/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__303868261998302__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"303868261998302","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2QIE/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__303868261998302__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd7dd0fceb31809b2e5eda/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd7dd0fceb31809b2e5eda/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd7dd0fceb31809b2e5eda/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/5cfd7dd0fceb31809b2e5eda/pdb.gz): 611 ms

reading 136 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

136 atoms created

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

Time for creating model: 18 ms

Adding embedded #jmolscript: select ({0:135});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	Staphylococcus aureus
publication title	Crystal structure of a molybdopterin synthase-precursor Z complex: insight into its sulfur transfer mechanism and its role in molybdenum cofactor deficiency. pubmed doi rcsb
molecule keywords	Molybdopterin-converting factor subunit 2
total genus	40
structure length	136
sequence length	136
chains with identical sequence	E, H, K
ec nomenclature	ec 2.8.1.12: Molybdopterin synthase.
pdb deposition date	2007-07-04

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02391	MoaE	MoaE protein

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

cath code	Class	Architecture	Topology	Homology	Domain
3.90.1170.40	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase; domain 3	Molybdopterin biosynthesis MoaE subunit	2qieA00

2QIEA 2Q5WE 4AP8A 1NVIE 3RPFA 1NVJA 2OMDA 2WP4A 3BIIE 1FMAE 5MPOC 1FM0E
chains in the Genus database with same CATH superfamily

3B9JC 2PA2A 5AYXA 5HUOA 2WP4A 4KWWA 3CCSH 3PIPJ 3H5QA 4LHMA 1YITH 2B7NA 1NJIJ 1M90J 4UY8M 3NVWC 3NVZC 3I55H 4IO9J 5DM6J 4WF9J 4YEKA 2OTJH 3BIIE 4X46A 1QPQA 3TQVA 5EY3A 1N8RJ 3CPWH 1QAPA 3I56H 1Q86J 3CC7H 1WKIA 3FC4A 1VQ9H 4YYYA 4IOCJ 5GADN 3GNNA 2B7PA 1JRPB 3EUB4 5H1SO 3CXCH 5GAGN 1YI2H 1KC8J 1K9MJ 2OTLH 1O4UA 3J7ZM 3CCQH 3C2EA 1VQ4H 1Q81J 1QVGH 2W3SB 3CCLH 1N63B 2JBMA 1QPNA 1SIJA 2ZJQJ 1W2BH 1KQSH 1FMAE 4C7YA 4WFNJ 2QEXH 1YJ9H 1VDVA 4AP8A 1VQMH 1JJ2H 3ETRC 3NRZC 4C7ZA 2DSJA 3AM9A 5HL7J 4KWVA 3PIOJ 3CC4H 5DM7J 3RPFA 1FO4A 1VQ5H 1OTPA 4US8A 3DLLJ 2B7QA 3CC2H 4WFAJ 4WCEJ 1NVJA 4IOAJ 2QA4H 1VQ6H 2WK6A 3G6EH 1QVFH 4GA5A 2TPTA 1DGJA 1QPRA 4GA6A 2OMDA 1YIJH 3WO1A 1ZXIB 1VQOH 3AN1A 1YTEA 4GA4A 1BRWA 1JROB 1KD1J 3WNZA 4C80A 3CCUH 1N60B 4ZOHA 3CCRH 1N61B 1FIQC 3C2OA 1FFVB 3C2RA 5MPOC 2W3RB 1RM6A 3NVVC 4U67J 1YTDA 1N62B 2Q5WE 3C2VA 5HULA 1AZYA 3L0GA 2ZJRJ 2I1OA 3AMZA 3CMEH 5GAHN 1YJNH 4US9A 2QIEA 1SB3A 1UOUA 2WK5A 2ZJPJ 5AYZA 2I14A 3CF5J 2E3TA 1WYGA 3L4PA 1VLBA 4XR5A 1VQ7H 1K8AJ 4WFBJ 3CCEH 1VQKH 1FFUB 1VQNH 3C2FA 5AN9F 1S72H 3NVYC 5JVHJ 3NS1C 1VQLH 1VQ8H 1NVIE 2W54B 3CCVH 1Y69K 3CD6H 1Q82J 3FAHA 3PAJA 1YHQH 3G71H 2J0FA 1K73J 2W55B 1V97A 1QPOA 1N5XA 5JVGJ 3CCMH 1X1OA 4EAFA 5EP8A 1Q7YJ 1YJWH 1VQPH 4USAA 4I9AA 5HUPA 3VMMA 5MLCO 1M1KJ 1YTKA 1FM0E 4EADA 3G4SH 3CCJH 3SR6C 3OW2H 5AYYA 3WO0A 5GAEN 1N5WB 3CMAH
chains in the Genus database with same CATH topology

2QIEA 2Q5WE 4AP8A 1NVIE 3RPFA 1NVJA 2OMDA 2WP4A 3BIIE 1FMAE 5MPOC 1FM0E
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2QIE A;  2Q5W E;  4AP8 A;  1NVI E;  3RPF A;  1NVJ A;  2OMD A;  2WP4 A;  3BII E;  1FMA E;  5MPO C;  1FM0 E; 
#chains in the Genus database with same CATH topology
 3B9J C;  2PA2 A;  5AYX A;  5HUO A;  2WP4 A;  4KWW A;  3CCS H;  3PIP J;  3H5Q A;  4LHM A;  1YIT H;  2B7N A;  1NJI J;  1M90 J;  4UY8 M;  3NVW C;  3NVZ C;  3I55 H;  4IO9 J;  5DM6 J;  4WF9 J;  4YEK A;  2OTJ H;  3BII E;  4X46 A;  1QPQ A;  3TQV A;  5EY3 A;  1N8R J;  3CPW H;  1QAP A;  3I56 H;  1Q86 J;  3CC7 H;  1WKI A;  3FC4 A;  1VQ9 H;  4YYY A;  4IOC J;  5GAD N;  3GNN A;  2B7P A;  1JRP B;  3EUB 4;  5H1S O;  3CXC H;  5GAG N;  1YI2 H;  1KC8 J;  1K9M J;  2OTL H;  1O4U A;  3J7Z M;  3CCQ H;  3C2E A;  1VQ4 H;  1Q81 J;  1QVG H;  2W3S B;  3CCL H;  1N63 B;  2JBM A;  1QPN A;  1SIJ A;  2ZJQ J;  1W2B H;  1KQS H;  1FMA E;  4C7Y A;  4WFN J;  2QEX H;  1YJ9 H;  1VDV A;  4AP8 A;  1VQM H;  1JJ2 H;  3ETR C;  3NRZ C;  4C7Z A;  2DSJ A;  3AM9 A;  5HL7 J;  4KWV A;  3PIO J;  3CC4 H;  5DM7 J;  3RPF A;  1FO4 A;  1VQ5 H;  1OTP A;  4US8 A;  3DLL J;  2B7Q A;  3CC2 H;  4WFA J;  4WCE J;  1NVJ A;  4IOA J;  2QA4 H;  1VQ6 H;  2WK6 A;  3G6E H;  1QVF H;  4GA5 A;  2TPT A;  1DGJ A;  1QPR A;  4GA6 A;  2OMD A;  1YIJ H;  3WO1 A;  1ZXI B;  1VQO H;  3AN1 A;  1YTE A;  4GA4 A;  1BRW A;  1JRO B;  1KD1 J;  3WNZ A;  4C80 A;  3CCU H;  1N60 B;  4ZOH A;  3CCR H;  1N61 B;  1FIQ C;  3C2O A;  1FFV B;  3C2R A;  5MPO C;  2W3R B;  1RM6 A;  3NVV C;  4U67 J;  1YTD A;  1N62 B;  2Q5W E;  3C2V A;  5HUL A;  1AZY A;  3L0G A;  2ZJR J;  2I1O A;  3AMZ A;  3CME H;  5GAH N;  1YJN H;  4US9 A;  2QIE A;  1SB3 A;  1UOU A;  2WK5 A;  2ZJP J;  5AYZ A;  2I14 A;  3CF5 J;  2E3T A;  1WYG A;  3L4P A;  1VLB A;  4XR5 A;  1VQ7 H;  1K8A J;  4WFB J;  3CCE H;  1VQK H;  1FFU B;  1VQN H;  3C2F A;  5AN9 F;  1S72 H;  3NVY C;  5JVH J;  3NS1 C;  1VQL H;  1VQ8 H;  1NVI E;  2W54 B;  3CCV H;  1Y69 K;  3CD6 H;  1Q82 J;  3FAH A;  3PAJ A;  1YHQ H;  3G71 H;  2J0F A;  1K73 J;  2W55 B;  1V97 A;  1QPO A;  1N5X A;  5JVG J;  3CCM H;  1X1O A;  4EAF A;  5EP8 A;  1Q7Y J;  1YJW H;  1VQP H;  4USA A;  4I9A A;  5HUP A;  3VMM A;  5MLC O;  1M1K J;  1YTK A;  1FM0 E;  4EAD A;  3G4S H;  3CCJ H;  3SR6 C;  3OW2 H;  5AYY A;  3WO0 A;  5GAE N;  1N5W B;  3CMA H; 
#chains in the Genus database with same CATH homology
 2QIE A;  2Q5W E;  4AP8 A;  1NVI E;  3RPF A;  1NVJ A;  2OMD A;  2WP4 A;  3BII E;  1FMA E;  5MPO C;  1FM0 E;

...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...

2QIEA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations