2FKM | Genus

Total Genus 170

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	170
sequence length	454
structure length	454
Chain Sequence	PASIFRAYDIRGVVGDTLTAETAYWIGRAIGSESLARGEPCVAVGRDGRLSGPELVKQLIQGLVDCGCQVSDVGMVPTPVLYYAANVLEGKSGVMLTGDHNPPDYNGFKIVVAGETLANEQIQALRERIEKNDLASGVGSVEQVDILPRYFKQIRDDIAMAKPMKVVVDCGNGVAGVIAPQLIEALGCSVIPLYCEVDGNFPNHHPDPGKPENLKDLIAKVKAENADLGLAFDGDGDRVGVVTNTGTIIYPDRLLMLFAKDVVSRNPGADIIFDVKCTRRLIALISGYGGRPVMWKTGHSLIKKKMKETGALLAGEMSGHVFFKERWFGFDDGIYSAARLLEILSQDQRDSEHVFSAFPSDISTPEINITVTEDSKFAIIEALQRDAQWGEGNITTLDGVRVDYPKGWGLVRASNTTPVLVLRFEADTEEELERIKTVFRNQLKAVDSSLPVPF

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__644767522375084__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__644767522375084__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2FKM/X/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__644767522375084__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"644767522375084","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2FKM/X/"

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__644767522375084__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfcff2e91f4d7b2f11005bf/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfcff2e91f4d7b2f11005bf/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfcff2e91f4d7b2f11005bf/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/5cfcff2e91f4d7b2f11005bf/pdb.gz): 283 ms

reading 454 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

454 atoms created

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

Time for creating model: 30 ms

Adding embedded #jmolscript: select ({0:453});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	Isomerase
source organism	Pseudomonas aeruginosa
publication title	The reaction of phosphohexomutase from Pseudomonas aeruginosa: structural insights into a simple processive enzyme. pubmed doi rcsb
molecule keywords	Phosphomannomutase/phosphoglucomutase
total genus	170
structure length	454
sequence length	454
ec nomenclature	ec 5.4.2.2: Phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent).
pdb deposition date	2006-01-04

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
X	PF00408	PGM_PMM_IV	Phosphoglucomutase/phosphomannomutase, C-terminal domain
X	PF02878	PGM_PMM_I	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
X	PF02879	PGM_PMM_II	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
X	PF02880	PGM_PMM_III	Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.310.50	Alpha Beta	2-Layer Sandwich	TATA-Binding Protein	Alpha-D-phosphohexomutase, C-terminal domain	2fkmX04
3.40.120.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3	Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3	2fkmX03
3.40.120.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3	Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3	2fkmX01
3.40.120.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3	Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3	2fkmX02

1PCJX 1VKLA 3PMGA 1P5DX 2H4LX 3OLPA 5KL0A 2DKAA 1PCMX 3NA5A 4QG5A 4IL8A 2F7LA 1C4GA 4MRQA 1KFQA 3BKQX 2FKFA 5JN5A 1WQAA 1WJWA 2EIUA 3PDKA 2JPIA 5BMNA 2H5AX 1K2YX 1K35A 1KFIA 1TUOA 3ENCA 4WXAA 2EHPA 2DKCA 5JMVD 4BJUA 2DKDA 5EPCA 3RSMA 2FKMX 1LXTA 5F9CA 3UW2A 2FUVA 1JDYA 3C04A 4HJHA 5BMPA 3I3WA 4WX8A 5HSHA 2Z0FA 3ENOC 1C47A 1P5GX
chains in the Genus database with same CATH superfamily

1KY7A 2NOHA 1VKLA 1VTLE 2R5XA 3TE5A 2FGTA 1R4XA 4EAJA 1LWVA 1PCMX 3RPJA 1CDWA 2NOLA 4ROCB 3EIKA 4QG5A 1QN5A 3HS9A 3T4NA 1C4GA 1QN3A 4MRQA 1YTFA 1QNEA 2LAEA 1DIZA 2V92A 1WQAA 1WJWA 1QNAA 1XSZA 3ASMA 3EAYA 1LWWA 1KYDA 1K2YX 1MP9A 2QRDA 3OSMA 1KFIA 5AN4A 4CFFA 3OH9A 1VTOA 1QNBA 1YQMA 3KRMA 3I0XA 3D4VA 2EHPA 3ULXA 2DKDA 1V5SA 1NH2A 5F9CA 2I5WA 3CW7A 1C9BB 3F10A 1YQRA 3C04A 5HSHA 4EAKA 1TGHA 2MZ8A 3DPTA 1C47A 1QN7A 1FN7A 1PCJX 3DPUA 1KY6A 3PMGA 1P5DX 1PVSA 2D0AA 3OSEA 2NOIA 1KFQA 2JHNA 2HKPA 2NWVA 1M3HA 1QN6A 1NGMA 3OC3C 4D7RA 1TBPA 3OH6A 2NOZA 2EIUA 1QN9A 3PDKA 1W80A 3KTUA 1N3AA 2V8QA 1D3UA 3N89A 1EBMA 2OOXA 1JFIC 3ENCA 3OGDA 4Q11A 2JOIA 1J3MA 5JMVD 2QRCA 4BJUA 5EPCA 3RSMA 1N3CA 1MPGA 4RODB 3UW2A 3HS8A 5IYBP 2JHJA 2FUVA 4HJHA 2YH5A 1Q9UA 4EALA 1VOLB 3BKQX 4D7QA 1T6AA 1YQLA 1QN8A 2Y8QA 3D7QA 3VN5A 4WZSD 3OLPA 2V9JA 1KO9A 2ZFDB 4EAIA 2Y8LA 2NOBA 2QREA 1KYUA 3CWAA 3NA5A 1TBAB 2HL9A 2D0BA 3CWSA 1QTPA 4TPSA 2FKFA 1NVPA 2HL8A 2OOYA 2YA3A 3OSTA 5JN5A 4ROEB 2QLVA 1M3QA 2JPIA 5BMNA 2H5AX 2VJ0A 1UL7A 2Z8UA 1QNCA 2QR1A 1HU0A 4WXAA 2DKCA 3TDHA 2HZSA 1YQKA 4C7PA 4PY5A 5IYCP 2O3OA 2NLVA 1LWYA 3I3WA 4WX8A 1VOKA 1AISA 2IV8A 2HZMA 3CWUA 2XHIA 2H4LX 5KL0A 1E42A 1PCZA 2DKAA 1UT7A 3CVSA 2NOEA 3F0ZA 4IL8A 2F7LA 4I8OA 1QN4A 2NOFA 1PZDA 5IYDP 2D0CA 1B9KA 1YTBA 1EUVA 2EHBD 1UT4A 1QTSA 3IH7A 1RM1A 1K35A 3OCIA 1TUOA 3CVTA 4B0AA 1M5Q1 1N39A 3CWTA 4EJYA 2MJ7A 3H1ZA 2IV9A 2NVMA 3SNSA 4EAGA 2PWWA 2FKMX 1LXTA 2G30A 3I0WA 4DULA 1KYFA 4EJZA 1JDYA 5BMPA 2Z0FA 3ENOC 1P5GX
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1PCJ X;  1VKL A;  3PMG A;  1P5D X;  2H4L X;  3OLP A;  5KL0 A;  2DKA A;  1PCM X;  3NA5 A;  4QG5 A;  4IL8 A;  2F7L A;  1C4G A;  4MRQ A;  1KFQ A;  3BKQ X;  2FKF A;  5JN5 A;  1WQA A;  1WJW A;  2EIU A;  3PDK A;  2JPI A;  5BMN A;  2H5A X;  1K2Y X;  1K35 A;  1KFI A;  1TUO A;  3ENC A;  4WXA A;  2EHP A;  2DKC A;  5JMV D;  4BJU A;  2DKD A;  5EPC A;  3RSM A;  2FKM X;  1LXT A;  5F9C A;  3UW2 A;  2FUV A;  1JDY A;  3C04 A;  4HJH A;  5BMP A;  3I3W A;  4WX8 A;  5HSH A;  2Z0F A;  3ENO C;  1C47 A;  1P5G X; 
#chains in the Genus database with same CATH topology
 1KY7 A;  2NOH A;  1VKL A;  1VTL E;  2R5X A;  3TE5 A;  2FGT A;  1R4X A;  4EAJ A;  1LWV A;  1PCM X;  3RPJ A;  1CDW A;  2NOL A;  4ROC B;  3EIK A;  4QG5 A;  1QN5 A;  3HS9 A;  3T4N A;  1C4G A;  1QN3 A;  4MRQ A;  1YTF A;  1QNE A;  2LAE A;  1DIZ A;  2V92 A;  1WQA A;  1WJW A;  1QNA A;  1XSZ A;  3ASM A;  3EAY A;  1LWW A;  1KYD A;  1K2Y X;  1MP9 A;  2QRD A;  3OSM A;  1KFI A;  5AN4 A;  4CFF A;  3OH9 A;  1VTO A;  1QNB A;  1YQM A;  3KRM A;  3I0X A;  3D4V A;  2EHP A;  3ULX A;  2DKD A;  1V5S A;  1NH2 A;  5F9C A;  2I5W A;  3CW7 A;  1C9B B;  3F10 A;  1YQR A;  3C04 A;  5HSH A;  4EAK A;  1TGH A;  2MZ8 A;  3DPT A;  1C47 A;  1QN7 A;  1FN7 A;  1PCJ X;  3DPU A;  1KY6 A;  3PMG A;  1P5D X;  1PVS A;  2D0A A;  3OSE A;  2NOI A;  1KFQ A;  2JHN A;  2HKP A;  2NWV A;  1M3H A;  1QN6 A;  1NGM A;  3OC3 C;  4D7R A;  1TBP A;  3OH6 A;  2NOZ A;  2EIU A;  1QN9 A;  3PDK A;  1W80 A;  3KTU A;  1N3A A;  2V8Q A;  1D3U A;  3N89 A;  1EBM A;  2OOX A;  1JFI C;  3ENC A;  3OGD A;  4Q11 A;  2JOI A;  1J3M A;  5JMV D;  2QRC A;  4BJU A;  5EPC A;  3RSM A;  1N3C A;  1MPG A;  4ROD B;  3UW2 A;  3HS8 A;  5IYB P;  2JHJ A;  2FUV A;  4HJH A;  2YH5 A;  1Q9U A;  4EAL A;  1VOL B;  3BKQ X;  4D7Q A;  1T6A A;  1YQL A;  1QN8 A;  2Y8Q A;  3D7Q A;  3VN5 A;  4WZS D;  3OLP A;  2V9J A;  1KO9 A;  2ZFD B;  4EAI A;  2Y8L A;  2NOB A;  2QRE A;  1KYU A;  3CWA A;  3NA5 A;  1TBA B;  2HL9 A;  2D0B A;  3CWS A;  1QTP A;  4TPS A;  2FKF A;  1NVP A;  2HL8 A;  2OOY A;  2YA3 A;  3OST A;  5JN5 A;  4ROE B;  2QLV A;  1M3Q A;  2JPI A;  5BMN A;  2H5A X;  2VJ0 A;  1UL7 A;  2Z8U A;  1QNC A;  2QR1 A;  1HU0 A;  4WXA A;  2DKC A;  3TDH A;  2HZS A;  1YQK A;  4C7P A;  4PY5 A;  5IYC P;  2O3O A;  2NLV A;  1LWY A;  3I3W A;  4WX8 A;  1VOK A;  1AIS A;  2IV8 A;  2HZM A;  3CWU A;  2XHI A;  2H4L X;  5KL0 A;  1E42 A;  1PCZ A;  2DKA A;  1UT7 A;  3CVS A;  2NOE A;  3F0Z A;  4IL8 A;  2F7L A;  4I8O A;  1QN4 A;  2NOF A;  1PZD A;  5IYD P;  2D0C A;  1B9K A;  1YTB A;  1EUV A;  2EHB D;  1UT4 A;  1QTS A;  3IH7 A;  1RM1 A;  1K35 A;  3OCI A;  1TUO A;  3CVT A;  4B0A A;  1M5Q 1;  1N39 A;  3CWT A;  4EJY A;  2MJ7 A;  3H1Z A;  2IV9 A;  2NVM A;  3SNS A;  4EAG A;  2PWW A;  2FKM X;  1LXT A;  2G30 A;  3I0W A;  4DUL A;  1KYF A;  4EJZ A;  1JDY A;  5BMP A;  2Z0F A;  3ENO C;  1P5G X; 
#chains in the Genus database with same CATH homology
 1PCJ X;  1VKL A;  3PMG A;  1P5D X;  2H4L X;  3OLP A;  5KL0 A;  2DKA A;  1PCM X;  3NA5 A;  4QG5 A;  4IL8 A;  2F7L A;  1C4G A;  4MRQ A;  1KFQ A;  3BKQ X;  2FKF A;  5JN5 A;  1WQA A;  1WJW A;  2EIU A;  3PDK A;  2JPI A;  5BMN A;  2H5A X;  1K2Y X;  1K35 A;  1KFI A;  1TUO A;  3ENC A;  4WXA A;  2EHP A;  2DKC A;  5JMV D;  4BJU A;  2DKD A;  5EPC A;  3RSM A;  2FKM X;  1LXT A;  5F9C A;  3UW2 A;  2FUV A;  1JDY A;  3C04 A;  4HJH A;  5BMP A;  3I3W A;  4WX8 A;  5HSH A;  2Z0F A;  3ENO C;  1C47 A;  1P5G X;

...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...

2FKMX

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

pfam database annotations