2J56 | Genus

Total Genus 31

Loading diagram...

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	31
Knots found	KnotProt 2.0: K
sequence length	125
structure length	124
Chain Sequence	TDPRAKWVPQDNDIQACDYWRHCSIDGNICDCSGGSLTNCPPGTKLATASVASCYNPTDGQSYLIAYRDCCGYNVSGRCPCLNTEGELPVYRPEFANDIIWCFGAEDDAMTYHCTISPIVGKAS

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__44268517767822__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__44268517767822__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/2j56/L/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__44268517767822__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"44268517767822","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/2j56/L/"

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__44268517767822__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5cfd3bdf712f60aed1d2e8ac/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5cfd3bdf712f60aed1d2e8ac/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5cfd3bdf712f60aed1d2e8ac/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/5cfd3bdf712f60aed1d2e8ac/pdb.gz): 1161 ms

reading 124 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

124 atoms created

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

Time for creating model: 19 ms

Adding embedded #jmolscript: select ({0:123});backbone only;select *;

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

publication title	Tracking X-Ray-Derived Redox Changes in Crystals of a Methylamine Dehydrogenase/Amicyanin Complex Using Single-Crystal Uv/Vis Microspectrophotometry. pubmed doi rcsb
molecule keywords	AMICYANIN
molecule tags	Oxidoreductase
total genus	31
structure length	124
sequence length	125
chains with identical sequence	M
other databases	KnotProt 2.0: K
ec nomenclature	ec 1.4.9.1: Methylamine dehydrogenase (amicyanin).
pdb deposition date	2006-09-12

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
L	PF02975	Me-amine-dh_L	Methylamine dehydrogenase, L chain

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

cath code	Class	Architecture	Topology	Homology	Domain
2.60.30.10	Mainly Beta	Sandwich	Electron Transport Ethylamine Dehydrogenase	Methylamine/Aralkylamine dehydrogenase light chain	2j56L00

2IUQD 4FA9C 3SJLC 2IURD 3PXWC 1MG3B 4L3GC 2AGXD 2J55L 3RN1C 4FB1C 4O1QC 4FA4C 2AGZD 2I0RD 4FAVC 2MADL 2AGYD 3ORVC 4L3HC 1MAFL 3RLMC 2HKMD 2HJ4D 2HXCD 2OK4D 3PXSC 2J57K 2I0SD 2MTAL 2OJYD 4L1QC 2GC4B 3RMZC 2AH1D 1MG2B 2AGLD 3L4OC 1MAEL 2GC7B 2BBKL 4FANC 2OK6D 4FA1C 4FA5C 3SWSC 1MDAL 3PXTC 3SLEC 2IUVD 2H3XB 2HJBD 2J56L 3RN0C 2IAAB 2AGWD 2Q7QD 2AH0D 3L4MC 3SXTC 2IUPD 4Y5RC 2OIZD 2I0TD 2H47B 2HKRD 3C75L 3SVWC 4K3IC
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 2IUQ D;  4FA9 C;  3SJL C;  2IUR D;  3PXW C;  1MG3 B;  4L3G C;  2AGX D;  2J55 L;  3RN1 C;  4FB1 C;  4O1Q C;  4FA4 C;  2AGZ D;  2I0R D;  4FAV C;  2MAD L;  2AGY D;  3ORV C;  4L3H C;  1MAF L;  3RLM C;  2HKM D;  2HJ4 D;  2HXC D;  2OK4 D;  3PXS C;  2J57 K;  2I0S D;  2MTA L;  2OJY D;  4L1Q C;  2GC4 B;  3RMZ C;  2AH1 D;  1MG2 B;  2AGL D;  3L4O C;  1MAE L;  2GC7 B;  2BBK L;  4FAN C;  2OK6 D;  4FA1 C;  4FA5 C;  3SWS C;  1MDA L;  3PXT C;  3SLE C;  2IUV D;  2H3X B;  2HJB D;  2J56 L;  3RN0 C;  2IAA B;  2AGW D;  2Q7Q D;  2AH0 D;  3L4M C;  3SXT C;  2IUP D;  4Y5R C;  2OIZ D;  2I0T D;  2H47 B;  2HKR D;  3C75 L;  3SVW C;  4K3I C; 
#chains in the Genus database with same CATH topology
 2IUQ D;  4FA9 C;  3SJL C;  2IUR D;  3PXW C;  1MG3 B;  4L3G C;  2AGX D;  2J55 L;  3RN1 C;  4FB1 C;  4O1Q C;  4FA4 C;  2AGZ D;  2I0R D;  4FAV C;  2MAD L;  2AGY D;  3ORV C;  4L3H C;  1MAF L;  3RLM C;  2HKM D;  2HJ4 D;  2HXC D;  2OK4 D;  3PXS C;  2J57 K;  2I0S D;  2MTA L;  2OJY D;  4L1Q C;  2GC4 B;  3RMZ C;  2AH1 D;  1MG2 B;  2AGL D;  3L4O C;  1MAE L;  2GC7 B;  2BBK L;  4FAN C;  2OK6 D;  4FA1 C;  4FA5 C;  3SWS C;  1MDA L;  3PXT C;  3SLE C;  2IUV D;  2H3X B;  2HJB D;  2J56 L;  3RN0 C;  2IAA B;  2AGW D;  2Q7Q D;  2AH0 D;  3L4M C;  3SXT C;  2IUP D;  4Y5R C;  2OIZ D;  2I0T D;  2H47 B;  2HKR D;  3C75 L;  3SVW C;  4K3I C; 
#chains in the Genus database with same CATH homology
 2IUQ D;  4FA9 C;  3SJL C;  2IUR D;  3PXW C;  1MG3 B;  4L3G C;  2AGX D;  2J55 L;  3RN1 C;  4FB1 C;  4O1Q C;  4FA4 C;  2AGZ D;  2I0R D;  4FAV C;  2MAD L;  2AGY D;  3ORV C;  4L3H C;  1MAF L;  3RLM C;  2HKM D;  2HJ4 D;  2HXC D;  2OK4 D;  3PXS C;  2J57 K;  2I0S D;  2MTA L;  2OJY D;  4L1Q C;  2GC4 B;  3RMZ C;  2AH1 D;  1MG2 B;  2AGL D;  3L4O C;  1MAE L;  2GC7 B;  2BBK L;  4FAN C;  2OK6 D;  4FA1 C;  4FA5 C;  3SWS C;  1MDA L;  3PXT C;  3SLE C;  2IUV D;  2H3X B;  2HJB D;  2J56 L;  3RN0 C;  2IAA B;  2AGW D;  2Q7Q D;  2AH0 D;  3L4M C;  3SXT C;  2IUP D;  4Y5R C;  2OIZ D;  2I0T D;  2H47 B;  2HKR D;  3C75 L;  3SVW C;  4K3I C;

1MG3B 2GC4B 2GC7B 2J55L 2J56L 2J57K 3L4MC 3L4OC 3ORVC
similar chains in the Genus database (40% sequence similarity)

None
similar chains in the pdb database (40% sequence similarity)

#similar chains in the Genus database (40% sequence similarity)
1MG3 B; 2GC4 B; 2GC7 B; 2J55 L; 2J56 L; 2J57 K; 3L4M C; 3L4O C; 3ORV C; 
#similar chains, but unknotted

#similar chains in the pdb database (40% sequence similarity)

2J56L

Total Genus

Knots found

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations