4KH3 | Genus

Total Genus 207

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	207
sequence length	500
structure length	492
Chain Sequence	ADIVVHPGETVNGGTLVNHDNQFVSGTANGVTVSTGLELGPDSDENTGGQWIKAGGTGRNTTVTANGRQIVQAGGTASDTVIRDGGGQSLNGLAVNTTLDNRGEQWVHGGGKAAGTIINQDGYQTIKHGGLATGTIVNTGAESSGQMVGGTAESTTINKNGRQVIWSSGMARDTLIYAGGDQTVHGEAHNTRLEGGNQYVHNGGTATETLINRDGWQVIKEGGTAAHTTINQKGKLQVNAGGKASDVTQNTGGALVTSTAATVTGTNRLGAFSVVAGKADNVVLENGGRLDVLSGHTATNTRVDDGGTLDIRNGGAATTVSMGNGGVLLADSGAAVSGTRSDGKAFSIGGGQADALMLEKGSSFTLNAGDTATDTTVNGGLFTARGGTLAGTTTLNNGAILTLSGKTVNNDTLTIREGDALLQGGSLTGNGSVEKSGSGTLTVSNTTLTQKAVNLNEGTLTLNDSTVTTDVIAQRGTALKLTGSTVLNGAID

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__093007111781576__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__093007111781576__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4KH3/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__093007111781576__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"093007111781576","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4KH3/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__093007111781576__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d00664a8718a54cfcad3d64/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d00664a8718a54cfcad3d64/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d00664a8718a54cfcad3d64/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/5d00664a8718a54cfcad3d64/pdb.gz): 164 ms

reading 492 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

492 atoms created

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

Time for creating model: 31 ms

Adding embedded #jmolscript: select ({0:491});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

molecule tags	Immune system
source organism	Escherichia coli
publication title	The antigen 43 structure reveals a molecular Velcro-like mechanism of autotransporter-mediated bacterial clumping. pubmed doi rcsb
molecule keywords	Antigen 43
total genus	207
structure length	492
sequence length	500
ec nomenclature
pdb deposition date	2013-04-30

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF16168	AIDA	Adhesin of bacterial autotransporter system, probable stalk

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

cath code	Class	Architecture	Topology	Homology	Domain
2.160.20.20	Mainly Beta	3 Solenoid	Pectate Lyase C-like	Pectate Lyase C-like	4kh3A00

1QA3A 1QRBA 1TSPA 1CLWA 3AK5A 3SYJA 1QA2A 3RIQA 2VFNA 3H09A 3ML3A 1QRCA 4KH3A 2VFMA 1QA1A 1TYUA 2VFOA 1WXRA 1TYXA 2V5IA 3TH0A 3SZEA 2IOUG 1TYVA 2XC1A 1QQ1A 4OM9A 1DABA 2VFPA 1TYWA 2VFQA
chains in the Genus database with same CATH superfamily

2VBEA 3PETA 3T9GA 3BH6B 1CLWA 2F3LA 3N6ZA 1PXZA 1OFLA 1RWRA 1CZFA 3N90A 4XKVA 2X3HA 2VFNA 3RIQA 1PLUA 2O6WA 1O8GA 2NTQA 3DU1X 4XMYA 3UW0A 1O8HA 2QYUA 4OJ6A 3EQOA 3NB2A 1O8MA 2J8KA 2VFMA 3FY3A 4I84A 3VSUA 2XT4A 3LYCA 1OFMA 2QXZA 4YZXA 1AIRA 1TYXA 2INVA 4YFOA 4Z05A 4XL9A 2O0WA 3TH0A 2VBMA 2IOUG 1PE9A 2X6YA 1KTWA 4XLAA 2O1DA 4XR6A 2UVFA 1QQ1A 4OZZA 2UVEA 4YELA 1RMGA 3SQVA 2VFQA 1IA5A 3B8YA 5C1EA 2BM6A 4EW9A 3P4GA 2W7ZA 4XORA 1O88A 3AK5A 1O8JA 4XQFA 1WMRA 2BM7A 2NSTA 4XKWA 4XOTA 2QY1A 2X85A 3SUCA 1IDJA 2J8IA 2B0RA 1KCDA 1L1IA 4W8QA 1QRCA 4OPWA 1OGMX 1QA1A 4XLCA 5DNSA 3WWGA 1K8FA 1K4ZA 1WXRA 1HG8A 2INUA 4W8RA 1QCXA 4YZAA 1LM1A 2V5IA 2G0YA 4OJ5A 1XG2A 1OOCA 1VBLA 3SZEA 4OZYA 2BSPA 2XTXA 4NK8A 4NK6A 1TYVA 2XC1A 2NZMA 2VBKA 2VFPA 2O0VA 4YDTA 4YEIA 3H09A 1JRGA 1QRBA 1EZGA 3GQ8A 4OJOA 1TSPA 5JMCB 4MR0A 4URRA 4PMHA 4OJLA 3PSSA 3ZSCA 4AVZA 1JTAA 1O8EA 1OFEA 1IDKA 3GQ7A 1O8DA 2O04A 2X6XA 4OJPA 4Z03A 1IB4A 4KH3A 2PYHA 5C1CA 4V02C 2NT6A 1OGOX 2VJJA 2BX6A 1O8LA 4MXNA 4C2LA 5JLVC 1TYUA 2XT2A 4XOPA 3GQ9A 2VFOA 3B90A 1O8FA 4XNFA 1KQ5A 4XLHA 4XLEA 3VMWA 4YCQA 4YZQA 1OFDA 3NAWA 1DBOA 1LLZA 2QX3A 2X6WA 4U4BA 1EA0A 4OM9A 1H80A 4XONA 4YC5A 2YUHA 4HWVA 2XTWA 1KCCA 1QA3A 1O8KA 2EWEA 3B4NA 3ZPPA 1QJVA 2NTPA 1HF2A 1RU4A 3SYJA 3KRGA 4W8SA 1QA2A 2BM5A 3JX8A 3ML3A 1EE6A 1GQ8A 2O17A 2BM4A 3GRHA 4Z06A 2QZAA 3VMVA 3VSVA 2NSPA 1O8IA 4XM3A 4U49A 4XLFA 3LMWA 4YZ0A 2PECA 3GQAA 4XN0A 3JURA 4XN3A 1LLWA 4YEJA 1BHEA 1X0CA 2NTBA 2NT9A 1NHCA 5AMVA 2ODLA 3PSZA 1K5CA 3LJYA 3SY2A 2VJIA 3BH7B 1DBGA 4JRAC 2IQ7A 3VSTA 2PYGA 1DABA 4W8TA 2XTYA 1TYWA 2Z8GA 3EQNA 1BN8A
chains in the Genus database with same CATH topology

1QA3A 1QRBA 3PETA 4OJOA 3BH6B 1TSPA 1CLWA 2F3LA 2W7ZA 3N6ZA 3P4GA 5JMCB 3AK5A 3N90A 1HF2A 4OJLA 3SYJA 2BM7A 1QA2A 3RIQA 2VFNA 2BM5A 3H09A 3JX8A 3ML3A 2J8IA 2B0RA 2BM4A 4OJPA 4OJ6A 1QRCA 4KH3A 4OPWA 2VFMA 4V02C 1QA1A 2BX6A 5JLVC 3LYCA 1TYUA 1K8FA 1K4ZA 2VFOA 1WXRA 1TYXA 1KQ5A 2V5IA 2G0YA 3LJYA 4OJ5A 3BH7B 4JRAC 3TH0A 3SZEA 2IOUG 1TYVA 2XC1A 1QQ1A 4OM9A 1DABA 2VFPA 2YUHA 1TYWA 2VFQA 2BM6A
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 1QA3 A;  1QRB A;  1TSP A;  1CLW A;  3AK5 A;  3SYJ A;  1QA2 A;  3RIQ A;  2VFN A;  3H09 A;  3ML3 A;  1QRC A;  4KH3 A;  2VFM A;  1QA1 A;  1TYU A;  2VFO A;  1WXR A;  1TYX A;  2V5I A;  3TH0 A;  3SZE A;  2IOU G;  1TYV A;  2XC1 A;  1QQ1 A;  4OM9 A;  1DAB A;  2VFP A;  1TYW A;  2VFQ A; 
#chains in the Genus database with same CATH topology
 2VBE A;  3PET A;  3T9G A;  3BH6 B;  1CLW A;  2F3L A;  3N6Z A;  1PXZ A;  1OFL A;  1RWR A;  1CZF A;  3N90 A;  4XKV A;  2X3H A;  2VFN A;  3RIQ A;  1PLU A;  2O6W A;  1O8G A;  2NTQ A;  3DU1 X;  4XMY A;  3UW0 A;  1O8H A;  2QYU A;  4OJ6 A;  3EQO A;  3NB2 A;  1O8M A;  2J8K A;  2VFM A;  3FY3 A;  4I84 A;  3VSU A;  2XT4 A;  3LYC A;  1OFM A;  2QXZ A;  4YZX A;  1AIR A;  1TYX A;  2INV A;  4YFO A;  4Z05 A;  4XL9 A;  2O0W A;  3TH0 A;  2VBM A;  2IOU G;  1PE9 A;  2X6Y A;  1KTW A;  4XLA A;  2O1D A;  4XR6 A;  2UVF A;  1QQ1 A;  4OZZ A;  2UVE A;  4YEL A;  1RMG A;  3SQV A;  2VFQ A;  1IA5 A;  3B8Y A;  5C1E A;  2BM6 A;  4EW9 A;  3P4G A;  2W7Z A;  4XOR A;  1O88 A;  3AK5 A;  1O8J A;  4XQF A;  1WMR A;  2BM7 A;  2NST A;  4XKW A;  4XOT A;  2QY1 A;  2X85 A;  3SUC A;  1IDJ A;  2J8I A;  2B0R A;  1KCD A;  1L1I A;  4W8Q A;  1QRC A;  4OPW A;  1OGM X;  1QA1 A;  4XLC A;  5DNS A;  3WWG A;  1K8F A;  1K4Z A;  1WXR A;  1HG8 A;  2INU A;  4W8R A;  1QCX A;  4YZA A;  1LM1 A;  2V5I A;  2G0Y A;  4OJ5 A;  1XG2 A;  1OOC A;  1VBL A;  3SZE A;  4OZY A;  2BSP A;  2XTX A;  4NK8 A;  4NK6 A;  1TYV A;  2XC1 A;  2NZM A;  2VBK A;  2VFP A;  2O0V A;  4YDT A;  4YEI A;  3H09 A;  1JRG A;  1QRB A;  1EZG A;  3GQ8 A;  4OJO A;  1TSP A;  5JMC B;  4MR0 A;  4URR A;  4PMH A;  4OJL A;  3PSS A;  3ZSC A;  4AVZ A;  1JTA A;  1O8E A;  1OFE A;  1IDK A;  3GQ7 A;  1O8D A;  2O04 A;  2X6X A;  4OJP A;  4Z03 A;  1IB4 A;  4KH3 A;  2PYH A;  5C1C A;  4V02 C;  2NT6 A;  1OGO X;  2VJJ A;  2BX6 A;  1O8L A;  4MXN A;  4C2L A;  5JLV C;  1TYU A;  2XT2 A;  4XOP A;  3GQ9 A;  2VFO A;  3B90 A;  1O8F A;  4XNF A;  1KQ5 A;  4XLH A;  4XLE A;  3VMW A;  4YCQ A;  4YZQ A;  1OFD A;  3NAW A;  1DBO A;  1LLZ A;  2QX3 A;  2X6W A;  4U4B A;  1EA0 A;  4OM9 A;  1H80 A;  4XON A;  4YC5 A;  2YUH A;  4HWV A;  2XTW A;  1KCC A;  1QA3 A;  1O8K A;  2EWE A;  3B4N A;  3ZPP A;  1QJV A;  2NTP A;  1HF2 A;  1RU4 A;  3SYJ A;  3KRG A;  4W8S A;  1QA2 A;  2BM5 A;  3JX8 A;  3ML3 A;  1EE6 A;  1GQ8 A;  2O17 A;  2BM4 A;  3GRH A;  4Z06 A;  2QZA A;  3VMV A;  3VSV A;  2NSP A;  1O8I A;  4XM3 A;  4U49 A;  4XLF A;  3LMW A;  4YZ0 A;  2PEC A;  3GQA A;  4XN0 A;  3JUR A;  4XN3 A;  1LLW A;  4YEJ A;  1BHE A;  1X0C A;  2NTB A;  2NT9 A;  1NHC A;  5AMV A;  2ODL A;  3PSZ A;  1K5C A;  3LJY A;  3SY2 A;  2VJI A;  3BH7 B;  1DBG A;  4JRA C;  2IQ7 A;  3VST A;  2PYG A;  1DAB A;  4W8T A;  2XTY A;  1TYW A;  2Z8G A;  3EQN A;  1BN8 A; 
#chains in the Genus database with same CATH homology
 1QA3 A;  1QRB A;  3PET A;  4OJO A;  3BH6 B;  1TSP A;  1CLW A;  2F3L A;  2W7Z A;  3N6Z A;  3P4G A;  5JMC B;  3AK5 A;  3N90 A;  1HF2 A;  4OJL A;  3SYJ A;  2BM7 A;  1QA2 A;  3RIQ A;  2VFN A;  2BM5 A;  3H09 A;  3JX8 A;  3ML3 A;  2J8I A;  2B0R A;  2BM4 A;  4OJP A;  4OJ6 A;  1QRC A;  4KH3 A;  4OPW A;  2VFM A;  4V02 C;  1QA1 A;  2BX6 A;  5JLV C;  3LYC A;  1TYU A;  1K8F A;  1K4Z A;  2VFO A;  1WXR A;  1TYX A;  1KQ5 A;  2V5I A;  2G0Y A;  3LJY A;  4OJ5 A;  3BH7 B;  4JRA C;  3TH0 A;  3SZE A;  2IOU G;  1TYV A;  2XC1 A;  1QQ1 A;  4OM9 A;  1DAB A;  2VFP A;  2YUH A;  1TYW A;  2VFQ A;  2BM6 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...

4KH3A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations