3HMT | Genus

Total Genus 25

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	25
sequence length	91
structure length	91
Chain Sequence	RNTIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIR

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__304050288949477__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__304050288949477__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3HMT/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__304050288949477__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"304050288949477","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3HMT/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__304050288949477__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cff107a8586470d9bcecd05/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cff107a8586470d9bcecd05/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cff107a8586470d9bcecd05/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/5cff107a8586470d9bcecd05/pdb.gz): 505 ms

reading 91 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

91 atoms created

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

Time for creating model: 16 ms

Adding embedded #jmolscript: select ({0:90});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	Hormone
source organism	Homo sapiens
publication title	Structural basis for agonism and antagonism of hepatocyte growth factor. pubmed doi rcsb
molecule keywords	Hepatocyte growth factor
total genus	25
structure length	91
sequence length	91
chains with identical sequence	B
ec nomenclature
pdb deposition date	2009-05-29

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00024	PAN_1	PAN domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.50.4.10	Alpha Beta	3-Layer(bba) Sandwich	Hepatocyte Growth Factor	Hepatocyte Growth Factor	3hmtA00

2YIOA 2Q8BA 2F83A 4DURA 4R1CA 2LL3A 4IUAA 3HN4A 5CT1A 4Z0EA 1W81A 4UV6A 5CS3A 3HMSA 3ZLEA 5CS1A 1NK1A 3SP8A 1YXEA 4Z0FA 4APLA 5EODA 1Z40A 2Q8AA 5CS9A 2LL4M 2Z8VA 1I8NA 2Y8RA 2Z8WA 4Z09A 2J8LA 5CSQA 3ZWZA 5I25A 2YIPA 4UAOA 4R19A 3SRIA 5CS5A 2QJ4A 3MKPA 5EOKA 4R1AA 1W8KA 1BHTA 2X2ZA 2HGFA 3SRJA 4APMA 1HKYA 2J8JA 3HMRA 5CP9A 3HMTA 5CT2A 2K13X 5COEA 5CT3A 4A5TS 1GP9A 1GMNA 2QJ2A 1GMOA 4R1BA 4Z0DA 2YILA
chains in the Genus database with same CATH superfamily

2YIOA 2Q8BA 2F83A 4YIZA 4DURA 4R1CA 2LL3A 4IUAA 3HN4A 5CT1A 4Z0EA 1W81A 4UV6A 5CS3A 3HMSA 3ZLEA 5CS1A 1NK1A 3SP8A 1YXEA 4Z0FA 4APLA 5EODA 1Z40A 2Q8AA 5CS9A 2LL4M 2Z8VA 1I8NA 2Y8RA 2Z8WA 4Z09A 2J8LA 5CSQA 3ZWZA 5I25A 2YIPA 4UAOA 4R19A 4YIVA 3SRIA 5CS5A 2QJ4A 3MKPA 2KL5A 5EOKA 4R1AA 1W8KA 1BHTA 2X2ZA 2HGFA 3SRJA 4APMA 1HKYA 2J8JA 3HMRA 5CP9A 3HMTA 5CT2A 2K13X 5COEA 5CT3A 4A5TS 1GP9A 1GMNA 2QJ2A 1GMOA 4R1BA 4Z0DA 2YILA
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 2YIO A;  2Q8B A;  2F83 A;  4DUR A;  4R1C A;  2LL3 A;  4IUA A;  3HN4 A;  5CT1 A;  4Z0E A;  1W81 A;  4UV6 A;  5CS3 A;  3HMS A;  3ZLE A;  5CS1 A;  1NK1 A;  3SP8 A;  1YXE A;  4Z0F A;  4APL A;  5EOD A;  1Z40 A;  2Q8A A;  5CS9 A;  2LL4 M;  2Z8V A;  1I8N A;  2Y8R A;  2Z8W A;  4Z09 A;  2J8L A;  5CSQ A;  3ZWZ A;  5I25 A;  2YIP A;  4UAO A;  4R19 A;  3SRI A;  5CS5 A;  2QJ4 A;  3MKP A;  5EOK A;  4R1A A;  1W8K A;  1BHT A;  2X2Z A;  2HGF A;  3SRJ A;  4APM A;  1HKY A;  2J8J A;  3HMR A;  5CP9 A;  3HMT A;  5CT2 A;  2K13 X;  5COE A;  5CT3 A;  4A5T S;  1GP9 A;  1GMN A;  2QJ2 A;  1GMO A;  4R1B A;  4Z0D A;  2YIL A; 
#chains in the Genus database with same CATH topology
 2YIO A;  2Q8B A;  2F83 A;  4YIZ A;  4DUR A;  4R1C A;  2LL3 A;  4IUA A;  3HN4 A;  5CT1 A;  4Z0E A;  1W81 A;  4UV6 A;  5CS3 A;  3HMS A;  3ZLE A;  5CS1 A;  1NK1 A;  3SP8 A;  1YXE A;  4Z0F A;  4APL A;  5EOD A;  1Z40 A;  2Q8A A;  5CS9 A;  2LL4 M;  2Z8V A;  1I8N A;  2Y8R A;  2Z8W A;  4Z09 A;  2J8L A;  5CSQ A;  3ZWZ A;  5I25 A;  2YIP A;  4UAO A;  4R19 A;  4YIV A;  3SRI A;  5CS5 A;  2QJ4 A;  3MKP A;  2KL5 A;  5EOK A;  4R1A A;  1W8K A;  1BHT A;  2X2Z A;  2HGF A;  3SRJ A;  4APM A;  1HKY A;  2J8J A;  3HMR A;  5CP9 A;  3HMT A;  5CT2 A;  2K13 X;  5COE A;  5CT3 A;  4A5T S;  1GP9 A;  1GMN A;  2QJ2 A;  1GMO A;  4R1B A;  4Z0D A;  2YIL A; 
#chains in the Genus database with same CATH homology
 2YIO A;  2Q8B A;  2F83 A;  4YIZ A;  4DUR A;  4R1C A;  2LL3 A;  4IUA A;  3HN4 A;  5CT1 A;  4Z0E A;  1W81 A;  4UV6 A;  5CS3 A;  3HMS A;  3ZLE A;  5CS1 A;  1NK1 A;  3SP8 A;  1YXE A;  4Z0F A;  4APL A;  5EOD A;  1Z40 A;  2Q8A A;  5CS9 A;  2LL4 M;  2Z8V A;  1I8N A;  2Y8R A;  2Z8W A;  4Z09 A;  2J8L A;  5CSQ A;  3ZWZ A;  5I25 A;  2YIP A;  4UAO A;  4R19 A;  4YIV A;  3SRI A;  5CS5 A;  2QJ4 A;  3MKP A;  2KL5 A;  5EOK A;  4R1A A;  1W8K A;  1BHT A;  2X2Z A;  2HGF A;  3SRJ A;  4APM A;  1HKY A;  2J8J A;  3HMR A;  5CP9 A;  3HMT A;  5CT2 A;  2K13 X;  5COE A;  5CT3 A;  4A5T S;  1GP9 A;  1GMN A;  2QJ2 A;  1GMO A;  4R1B A;  4Z0D A;  2YIL 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...

3HMTA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations