1GP9 | Genus

Total Genus 37

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	37
sequence length	170
structure length	170
Chain Sequence	VHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSE

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__856959838900974__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__856959838900974__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/1GP9/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__856959838900974__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"856959838900974","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/1GP9/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__856959838900974__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfb3adfb3924d457152fdfd/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfb3adfb3924d457152fdfd/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfb3adfb3924d457152fdfd/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/5cfb3adfb3924d457152fdfd/pdb.gz): 542 ms

reading 170 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

170 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:169});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/growth factor
source organism	Homo sapiens
publication title	A New Crystal Form of the Nk1 Splice Variant of Hgf/Sf Demonstrates Extensive Hinge Movement and Suggests that the Nk1 Dimer Originates by Domain Swapping pubmed doi rcsb
molecule keywords	HEPATOCYTE GROWTH FACTOR
total genus	37
structure length	170
sequence length	170
chains with identical sequence	B, C, D
ec nomenclature
pdb deposition date	2001-10-31

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00024	PAN_1	PAN domain
A	PF00051	Kringle	Kringle domain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.40.20.10	Mainly Beta	Beta Barrel	Plasminogen Kringle 4	Plasminogen Kringle 4	1gp9A02
3.50.4.10	Alpha Beta	3-Layer(bba) Sandwich	Hepatocyte Growth Factor	Hepatocyte Growth Factor	1gp9A01

2DOIA 2YIPA 2YIOA 4R19A 4CIKA 2PF2A 1CEBA 1KIVA 1I71A 4NZQA 2Z8WA 2F83A 3LAQA 2FEBA 2KJ4A 4UV6A 2K51A 3HMRA 5HPGA 2PF1A 3SRIA 3K65A 4HZHA 1CEAA 1NK1A 2J8JA 3HMTA 4BVVA 3SP8A 5CT3A 1PK4A 2Q8BA 5CS9A 1BHTA 4R1AA 1URKA 5EOKA 4BV7A 5CS1A 3HMSA 1KI0A 4D3CA 2Y8RA 4BVDA 5EODA 2L0SA 3ZLEA 1W81A 1A0HA 4R1CA 4O03A 2KNFA 4R1BA 3HN4A 1I8NA 2SPTA 3MKPA 1YXEA 1PMLA 2J8LA 2I9AA 5I25A 4KIVA 1GP9A 2I9BA 1PK2A 4Z09A 4Z0EA 5CT2A 4APLA 1B2IA 2PK4A 4IUAA 2K13X 4UAOA 3U73A 2QJ4A 1NL2A 1HPJA 3KIVA 1KDUA 1PKRA 5CS5A 1GMOA 2QJ2A 2DOHX 1Z40A 1KRNA 3SRJA 4APMA 5CS3A 2Z8VA 5CSQA 2HPPP 1TPKA 2X2ZA 4BV5A 3BT1A 1PMKA 5COEA 4BVCA 2HPQP 2LL3A 2YILA 3ZWZA 1JFNA 5CT1A 1HKYA 2FD6A 2K4RA 3BT2A 3NXPA 2LL4M 5CP9A 1HPKA 3E6PL 4A5TS 4Z0FA 1NL1A 4BVWA 4Z0DA 2HGFA 1GMNA 1W8KA 1I5KA 4DURA 2Q8AA
chains in the Genus database with same CATH superfamily

2DOIA 2YIPA 2YIOA 4R19A 4CIKA 2PF2A 1CEBA 1KIVA 1I71A 4NZQA 2Z8WA 2F83A 3LAQA 2FEBA 2KJ4A 4UV6A 2K51A 3HMRA 5HPGA 2PF1A 3SRIA 3K65A 4HZHA 1CEAA 1NK1A 2J8JA 3HMTA 4BVVA 3SP8A 5CT3A 1PK4A 2Q8BA 5CS9A 1BHTA 4R1AA 1URKA 5EOKA 4BV7A 5CS1A 3HMSA 1KI0A 4D3CA 2Y8RA 4BVDA 5EODA 2L0SA 3ZLEA 1W81A 1A0HA 4R1CA 4O03A 2KNFA 4R1BA 3HN4A 1I8NA 2SPTA 3MKPA 1YXEA 1PMLA 2J8LA 2I9AA 5I25A 4KIVA 1GP9A 2I9BA 1PK2A 4Z09A 4Z0EA 5CT2A 4APLA 1B2IA 2PK4A 4IUAA 2K13X 4UAOA 3U73A 2QJ4A 1NL2A 1HPJA 3KIVA 1KDUA 1PKRA 5CS5A 1GMOA 2QJ2A 2DOHX 1Z40A 1KRNA 3SRJA 4APMA 5CS3A 2Z8VA 5CSQA 2HPPP 1TPKA 2X2ZA 4BV5A 3BT1A 4YIZA 1PMKA 5COEA 4BVCA 2HPQP 2LL3A 2YILA 3ZWZA 1JFNA 5CT1A 1HKYA 2FD6A 2K4RA 3BT2A 3NXPA 2LL4M 5CP9A 1HPKA 3E6PL 4A5TS 4Z0FA 1NL1A 4BVWA 2KL5A 2HGFA 1GMNA 1W8KA 4Z0DA 1I5KA 4YIVA 4DURA 2Q8AA
chains in the Genus database with same CATH topology

2DOIA 2YIPA 2YIOA 4R19A 4CIKA 2PF2A 1CEBA 1KIVA 1I71A 4NZQA 2Z8WA 2F83A 3LAQA 2FEBA 2KJ4A 4UV6A 2K51A 3HMRA 5HPGA 2PF1A 3SRIA 3K65A 4HZHA 1CEAA 1NK1A 2J8JA 3HMTA 4BVVA 3SP8A 5CT3A 1PK4A 2Q8BA 5CS9A 1BHTA 4R1AA 1URKA 5EOKA 4BV7A 5CS1A 3HMSA 1KI0A 4D3CA 2Y8RA 4BVDA 5EODA 2L0SA 3ZLEA 1W81A 1A0HA 4R1CA 4O03A 2KNFA 4R1BA 3HN4A 1I8NA 2SPTA 3MKPA 1YXEA 1PMLA 2J8LA 2I9AA 5I25A 4KIVA 1GP9A 2I9BA 1PK2A 4Z09A 4Z0EA 5CT2A 4APLA 1B2IA 2PK4A 4IUAA 2K13X 4UAOA 3U73A 2QJ4A 1NL2A 1HPJA 3KIVA 1KDUA 1PKRA 5CS5A 1GMOA 2QJ2A 2DOHX 1Z40A 1KRNA 3SRJA 4APMA 5CS3A 2Z8VA 5CSQA 2HPPP 1TPKA 2X2ZA 4BV5A 3BT1A 4YIZA 1PMKA 5COEA 4BVCA 2HPQP 2LL3A 2YILA 3ZWZA 1JFNA 5CT1A 1HKYA 2FD6A 2K4RA 3BT2A 3NXPA 2LL4M 5CP9A 1HPKA 3E6PL 4A5TS 4Z0FA 1NL1A 4BVWA 2KL5A 2HGFA 1GMNA 1W8KA 4Z0DA 1I5KA 4YIVA 4DURA 2Q8AA
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 2DOI A;  2YIP A;  2YIO A;  4R19 A;  4CIK A;  2PF2 A;  1CEB A;  1KIV A;  1I71 A;  4NZQ A;  2Z8W A;  2F83 A;  3LAQ A;  2FEB A;  2KJ4 A;  4UV6 A;  2K51 A;  3HMR A;  5HPG A;  2PF1 A;  3SRI A;  3K65 A;  4HZH A;  1CEA A;  1NK1 A;  2J8J A;  3HMT A;  4BVV A;  3SP8 A;  5CT3 A;  1PK4 A;  2Q8B A;  5CS9 A;  1BHT A;  4R1A A;  1URK A;  5EOK A;  4BV7 A;  5CS1 A;  3HMS A;  1KI0 A;  4D3C A;  2Y8R A;  4BVD A;  5EOD A;  2L0S A;  3ZLE A;  1W81 A;  1A0H A;  4R1C A;  4O03 A;  2KNF A;  4R1B A;  3HN4 A;  1I8N A;  2SPT A;  3MKP A;  1YXE A;  1PML A;  2J8L A;  2I9A A;  5I25 A;  4KIV A;  1GP9 A;  2I9B A;  1PK2 A;  4Z09 A;  4Z0E A;  5CT2 A;  4APL A;  1B2I A;  2PK4 A;  4IUA A;  2K13 X;  4UAO A;  3U73 A;  2QJ4 A;  1NL2 A;  1HPJ A;  3KIV A;  1KDU A;  1PKR A;  5CS5 A;  1GMO A;  2QJ2 A;  2DOH X;  1Z40 A;  1KRN A;  3SRJ A;  4APM A;  5CS3 A;  2Z8V A;  5CSQ A;  2HPP P;  1TPK A;  2X2Z A;  4BV5 A;  3BT1 A;  1PMK A;  5COE A;  4BVC A;  2HPQ P;  2LL3 A;  2YIL A;  3ZWZ A;  1JFN A;  5CT1 A;  1HKY A;  2FD6 A;  2K4R A;  3BT2 A;  3NXP A;  2LL4 M;  5CP9 A;  1HPK A;  3E6P L;  4A5T S;  4Z0F A;  1NL1 A;  4BVW A;  4Z0D A;  2HGF A;  1GMN A;  1W8K A;  1I5K A;  4DUR A;  2Q8A A; 
#chains in the Genus database with same CATH topology
 2DOI A;  2YIP A;  2YIO A;  4R19 A;  4CIK A;  2PF2 A;  1CEB A;  1KIV A;  1I71 A;  4NZQ A;  2Z8W A;  2F83 A;  3LAQ A;  2FEB A;  2KJ4 A;  4UV6 A;  2K51 A;  3HMR A;  5HPG A;  2PF1 A;  3SRI A;  3K65 A;  4HZH A;  1CEA A;  1NK1 A;  2J8J A;  3HMT A;  4BVV A;  3SP8 A;  5CT3 A;  1PK4 A;  2Q8B A;  5CS9 A;  1BHT A;  4R1A A;  1URK A;  5EOK A;  4BV7 A;  5CS1 A;  3HMS A;  1KI0 A;  4D3C A;  2Y8R A;  4BVD A;  5EOD A;  2L0S A;  3ZLE A;  1W81 A;  1A0H A;  4R1C A;  4O03 A;  2KNF A;  4R1B A;  3HN4 A;  1I8N A;  2SPT A;  3MKP A;  1YXE A;  1PML A;  2J8L A;  2I9A A;  5I25 A;  4KIV A;  1GP9 A;  2I9B A;  1PK2 A;  4Z09 A;  4Z0E A;  5CT2 A;  4APL A;  1B2I A;  2PK4 A;  4IUA A;  2K13 X;  4UAO A;  3U73 A;  2QJ4 A;  1NL2 A;  1HPJ A;  3KIV A;  1KDU A;  1PKR A;  5CS5 A;  1GMO A;  2QJ2 A;  2DOH X;  1Z40 A;  1KRN A;  3SRJ A;  4APM A;  5CS3 A;  2Z8V A;  5CSQ A;  2HPP P;  1TPK A;  2X2Z A;  4BV5 A;  3BT1 A;  4YIZ A;  1PMK A;  5COE A;  4BVC A;  2HPQ P;  2LL3 A;  2YIL A;  3ZWZ A;  1JFN A;  5CT1 A;  1HKY A;  2FD6 A;  2K4R A;  3BT2 A;  3NXP A;  2LL4 M;  5CP9 A;  1HPK A;  3E6P L;  4A5T S;  4Z0F A;  1NL1 A;  4BVW A;  2KL5 A;  2HGF A;  1GMN A;  1W8K A;  4Z0D A;  1I5K A;  4YIV A;  4DUR A;  2Q8A A; 
#chains in the Genus database with same CATH homology
 2DOI A;  2YIP A;  2YIO A;  4R19 A;  4CIK A;  2PF2 A;  1CEB A;  1KIV A;  1I71 A;  4NZQ A;  2Z8W A;  2F83 A;  3LAQ A;  2FEB A;  2KJ4 A;  4UV6 A;  2K51 A;  3HMR A;  5HPG A;  2PF1 A;  3SRI A;  3K65 A;  4HZH A;  1CEA A;  1NK1 A;  2J8J A;  3HMT A;  4BVV A;  3SP8 A;  5CT3 A;  1PK4 A;  2Q8B A;  5CS9 A;  1BHT A;  4R1A A;  1URK A;  5EOK A;  4BV7 A;  5CS1 A;  3HMS A;  1KI0 A;  4D3C A;  2Y8R A;  4BVD A;  5EOD A;  2L0S A;  3ZLE A;  1W81 A;  1A0H A;  4R1C A;  4O03 A;  2KNF A;  4R1B A;  3HN4 A;  1I8N A;  2SPT A;  3MKP A;  1YXE A;  1PML A;  2J8L A;  2I9A A;  5I25 A;  4KIV A;  1GP9 A;  2I9B A;  1PK2 A;  4Z09 A;  4Z0E A;  5CT2 A;  4APL A;  1B2I A;  2PK4 A;  4IUA A;  2K13 X;  4UAO A;  3U73 A;  2QJ4 A;  1NL2 A;  1HPJ A;  3KIV A;  1KDU A;  1PKR A;  5CS5 A;  1GMO A;  2QJ2 A;  2DOH X;  1Z40 A;  1KRN A;  3SRJ A;  4APM A;  5CS3 A;  2Z8V A;  5CSQ A;  2HPP P;  1TPK A;  2X2Z A;  4BV5 A;  3BT1 A;  4YIZ A;  1PMK A;  5COE A;  4BVC A;  2HPQ P;  2LL3 A;  2YIL A;  3ZWZ A;  1JFN A;  5CT1 A;  1HKY A;  2FD6 A;  2K4R A;  3BT2 A;  3NXP A;  2LL4 M;  5CP9 A;  1HPK A;  3E6P L;  4A5T S;  4Z0F A;  1NL1 A;  4BVW A;  2KL5 A;  2HGF A;  1GMN A;  1W8K A;  4Z0D A;  1I5K A;  4YIV A;  4DUR A;  2Q8A 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...

1GP9A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations