3AEV | Genus

Total Genus 61

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	61
sequence length	183
structure length	177
Chain Sequence	DEWEEFFKQEEYVKIPKDRIAVLIGKKGQTKKEIEKRTKTKITIDSETGEVWITSTKETEDPLAVWKARDIVLAIGRGFSPERAFRLLNEGEYLEIINLTDIIALPRVRGRIIGRKGRTRQIIEEMSGASVSVYGKTVAIIGNPIQIEIAKTAIEKLARGSPHGSVYRYLERRKKDL

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__525913508041343__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__525913508041343__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3AEV/B/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__525913508041343__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"525913508041343","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3AEV/B/"

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__525913508041343__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d2640e3f1043fe711db02e4/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d2640e3f1043fe711db02e4/pdb.gz

FileManager.getAtomSetCollectionFromFile(/file/5d2640e3f1043fe711db02e4/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/5d2640e3f1043fe711db02e4/pdb.gz): 747 ms

reading 177 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

177 atoms created

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

Time for creating model: 36 ms

Adding embedded #jmolscript: select ({0:176});backbone only;select *;

platformSpeed = 8

cartoonsFancy = true

sheetSmoothing = 1.0

traceAlpha = true

loadScript /static/js/j2s/core/corescriptcmd.z.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	Translation/rna binding protein/rna
source organism	Pyrococcus horikoshii
publication title	An archaeal Dim2-like protein, aDim2p, forms a ternary complex with a/eIF2 alpha and the 3' end fragment of 16S rRNA pubmed doi rcsb
molecule keywords	Translation initiation factor 2 subunit alpha
total genus	61
structure length	177
sequence length	183
ec nomenclature
pdb deposition date	2010-02-10

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
B	PF00013	KH_1	KH domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8; Chain: A, domain 1	K Homology domain, type 1	3aevB01
3.30.1370.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8; Chain: A, domain 1	K Homology domain, type 1	3aevB02

1VIGA 2AXYA 2CTEA 1ZZJA 1EC6A 2JE6I 2MJHA 2QNDA 2OPVA 1J4WA 1VIHA 2HH3A 1TUAA 2CTFA 3V69A 2ANNA 2BL5A 2JEBI 1ZTGA 4IFDG 2JA9A 2E3UA 3U1KA 4BA1I 2OPUA 2JEAI 1J5KA 1DTJA 5K36G 1X4NA 3VKEA 1KHMA 2ANRA 2NN6G 1ZZIA 4LIJA 4WALA 3L7ZC 2CPQA 2Z0SA 2CTMA 2BA0A 2YQRA 2PQUA 2P2RA 4B8TA 2JZXA 2CTJA 2PY9A 2CTLA 4AM3A 4WANA 2CTKA 4JVHA 1X4MA 2FMRA 5JEAG 1K1GA 2DGRA 4OO1G 4BA2I 1DT4A 4QMFB 3AEVB 1WE8A 2JVZA 4JVYA 5C0XG 1ZZKA 2HH2A 4AIMA 4NBQA 1WVNA
chains in the Genus database with same CATH superfamily

3T1HH 4JI1H 1VIGA 1MSZA 2AXYA 4DR7H 2JE6I 4YY3H 1TUAA 2CTFA 3V69A 4DV0H 2ANNA 2BL5A 1XRHA 5IWAH 4LF8H 3T1YH 4GKKH 4B3MH 2E3UA 2PT7G 4EC5A 1ODHA 4DR3H 4JI3H 2JEAI 1I6UA 4JI5H 4FJSA 1HR0H 2FPHX 1Z2IA 4PDBA 4X64H 3OTOH 3L7ZC 2YQRA 2BA0A 4OD6A 4AM3A 1XMQH 1IBKH 3GR5A 4WANA 4DV5H 2DGRA 1N36H 5BR8H 4BA2I 5DT9A 4QMFB 2A1SA 3QD7X 1WE8A 2JVZA 3KDKA 1WVNA 3EZJA 1J5EH 1UG8A 2CPMA 2CTEA 5LMUH 1ZZJA 1VBIA 1IBMH 2HH3A 4DV2H 2JEBI 4IFDG 2JA9A 4X66H 5K36G 2UUBH 2UXBH 1J5KA 1X4NA 3VKEA 4OX9H 4YHHH 2ANRA 1KHMA 1ZZIA 1X9ZA 2M8WA 4WALA 2UUCH 1XMOH 2CPQA 2Z0SA 4FJUA 4JI8H 2UUAH 4B8CD 2PQUA 2PY9A 2JZXA 2CTKA 3GABA 1K1GA 2X06A 4E9JA 4DV3H 2LTMA 4NZRM 4DUZH 4OCHA 4NXNH 1SEIA 2M6QA 5LL6b 5LMNH 1ZZKA 3JAMW 4LFBH 1NXUA 2E5LH 4DUYH 1EC6A 2UU9H 2MJHA 2OPVA 1J4WA 1VIHA 1N33H 4K0KH 1XNQH 2O4CA 3SB1A 4AQYH 4KHPH 4X62H 2D9IA 3GKUA 4DV6H 1I94H 4JI6H 1DTJA 4DV7H 1F0XA 1FKAH 4LF4H 2LTLA 2NN6G 3J81W 4DR4H 2CWFA 4B3TH 2UXDH 4DR2H 1XNRH 2P2RA 2CTJA 1IBLH 2VQFH 4JI7H 4NXMH 1FJGH 4JVHA 1X4MA 2FMRA 2UXCH 4DV4H 2LF0A 4JYAH 1DT4A 5A2QW 3AEVB 4NZTM 4DR5H 2Y3MA 4JI0H 4LF9H 4JVYA 3RF2A 4DV1H 1X0AA 4GKJH 1AN7A 1WHRA 4BA1I 4DR6H 1HNWH 1WTJA 2F4VH 3J80W 4JI4H 4DR1H 3OSSD 2ZM6H 4X65H 4B3RH 2QNDA 2VKCA 4H8AA 2HHHH 1V8CA 1ZTGA 2K1HA 4LF6H 3U1KA 2ZQEA 2OPUA 3UOEA 2VQEH 1S20A 4G08A 3J7AK 4LFAH 2G8YA 4LIJA 5FLXW 3FAUA 3I0PA 2CTMA 4LF5H 5IT9W 4B8TA 2CTLA 1HNXH 3KDGA 2FFMA 5JEAG 4JV5H 4OO1G 1N34H 1S03G 4LF7H 1PQXA 2LRRA 4JI2H 2CWHA 1HNZH 5C0XG 2HH2A 3OETA 4AIMA 4B3SH 4NBQA 4LFCH 3NCVA 1V9NA 1N32H
chains in the Genus database with same CATH topology

#chains in the Genus database with same CATH superfamily
 1VIG A;  2AXY A;  2CTE A;  1ZZJ A;  1EC6 A;  2JE6 I;  2MJH A;  2QND A;  2OPV A;  1J4W A;  1VIH A;  2HH3 A;  1TUA A;  2CTF A;  3V69 A;  2ANN A;  2BL5 A;  2JEB I;  1ZTG A;  4IFD G;  2JA9 A;  2E3U A;  3U1K A;  4BA1 I;  2OPU A;  2JEA I;  1J5K A;  1DTJ A;  5K36 G;  1X4N A;  3VKE A;  1KHM A;  2ANR A;  2NN6 G;  1ZZI A;  4LIJ A;  4WAL A;  3L7Z C;  2CPQ A;  2Z0S A;  2CTM A;  2BA0 A;  2YQR A;  2PQU A;  2P2R A;  4B8T A;  2JZX A;  2CTJ A;  2PY9 A;  2CTL A;  4AM3 A;  4WAN A;  2CTK A;  4JVH A;  1X4M A;  2FMR A;  5JEA G;  1K1G A;  2DGR A;  4OO1 G;  4BA2 I;  1DT4 A;  4QMF B;  3AEV B;  1WE8 A;  2JVZ A;  4JVY A;  5C0X G;  1ZZK A;  2HH2 A;  4AIM A;  4NBQ A;  1WVN A; 
#chains in the Genus database with same CATH topology
 3T1H H;  4JI1 H;  1VIG A;  1MSZ A;  2AXY A;  4DR7 H;  2JE6 I;  4YY3 H;  1TUA A;  2CTF A;  3V69 A;  4DV0 H;  2ANN A;  2BL5 A;  1XRH A;  5IWA H;  4LF8 H;  3T1Y H;  4GKK H;  4B3M H;  2E3U A;  2PT7 G;  4EC5 A;  1ODH A;  4DR3 H;  4JI3 H;  2JEA I;  1I6U A;  4JI5 H;  4FJS A;  1HR0 H;  2FPH X;  1Z2I A;  4PDB A;  4X64 H;  3OTO H;  3L7Z C;  2YQR A;  2BA0 A;  4OD6 A;  4AM3 A;  1XMQ H;  1IBK H;  3GR5 A;  4WAN A;  4DV5 H;  2DGR A;  1N36 H;  5BR8 H;  4BA2 I;  5DT9 A;  4QMF B;  2A1S A;  3QD7 X;  1WE8 A;  2JVZ A;  3KDK A;  1WVN A;  3EZJ A;  1J5E H;  1UG8 A;  2CPM A;  2CTE A;  5LMU H;  1ZZJ A;  1VBI A;  1IBM H;  2HH3 A;  4DV2 H;  2JEB I;  4IFD G;  2JA9 A;  4X66 H;  5K36 G;  2UUB H;  2UXB H;  1J5K A;  1X4N A;  3VKE A;  4OX9 H;  4YHH H;  2ANR A;  1KHM A;  1ZZI A;  1X9Z A;  2M8W A;  4WAL A;  2UUC H;  1XMO H;  2CPQ A;  2Z0S A;  4FJU A;  4JI8 H;  2UUA H;  4B8C D;  2PQU A;  2PY9 A;  2JZX A;  2CTK A;  3GAB A;  1K1G A;  2X06 A;  4E9J A;  4DV3 H;  2LTM A;  4NZR M;  4DUZ H;  4OCH A;  4NXN H;  1SEI A;  2M6Q A;  5LL6 b;  5LMN H;  1ZZK A;  3JAM W;  4LFB H;  1NXU A;  2E5L H;  4DUY H;  1EC6 A;  2UU9 H;  2MJH A;  2OPV A;  1J4W A;  1VIH A;  1N33 H;  4K0K H;  1XNQ H;  2O4C A;  3SB1 A;  4AQY H;  4KHP H;  4X62 H;  2D9I A;  3GKU A;  4DV6 H;  1I94 H;  4JI6 H;  1DTJ A;  4DV7 H;  1F0X A;  1FKA H;  4LF4 H;  2LTL A;  2NN6 G;  3J81 W;  4DR4 H;  2CWF A;  4B3T H;  2UXD H;  4DR2 H;  1XNR H;  2P2R A;  2CTJ A;  1IBL H;  2VQF H;  4JI7 H;  4NXM H;  1FJG H;  4JVH A;  1X4M A;  2FMR A;  2UXC H;  4DV4 H;  2LF0 A;  4JYA H;  1DT4 A;  5A2Q W;  3AEV B;  4NZT M;  4DR5 H;  2Y3M A;  4JI0 H;  4LF9 H;  4JVY A;  3RF2 A;  4DV1 H;  1X0A A;  4GKJ H;  1AN7 A;  1WHR A;  4BA1 I;  4DR6 H;  1HNW H;  1WTJ A;  2F4V H;  3J80 W;  4JI4 H;  4DR1 H;  3OSS D;  2ZM6 H;  4X65 H;  4B3R H;  2QND A;  2VKC A;  4H8A A;  2HHH H;  1V8C A;  1ZTG A;  2K1H A;  4LF6 H;  3U1K A;  2ZQE A;  2OPU A;  3UOE A;  2VQE H;  1S20 A;  4G08 A;  3J7A K;  4LFA H;  2G8Y A;  4LIJ A;  5FLX W;  3FAU A;  3I0P A;  2CTM A;  4LF5 H;  5IT9 W;  4B8T A;  2CTL A;  1HNX H;  3KDG A;  2FFM A;  5JEA G;  4JV5 H;  4OO1 G;  1N34 H;  1S03 G;  4LF7 H;  1PQX A;  2LRR A;  4JI2 H;  2CWH A;  1HNZ H;  5C0X G;  2HH2 A;  3OET A;  4AIM A;  4B3S H;  4NBQ A;  4LFC H;  3NCV A;  1V9N A;  1N32 H; 
#chains in the Genus database with same CATH homology
 1VIG A;  2AXY A;  2CTE A;  1ZZJ A;  1EC6 A;  2JE6 I;  2MJH A;  2QND A;  2OPV A;  1J4W A;  1VIH A;  2HH3 A;  1TUA A;  2CTF A;  3V69 A;  2ANN A;  2BL5 A;  2JEB I;  1ZTG A;  4IFD G;  2JA9 A;  2E3U A;  3U1K A;  4BA1 I;  2OPU A;  2JEA I;  1J5K A;  1DTJ A;  5K36 G;  1X4N A;  3VKE A;  1KHM A;  2ANR A;  2NN6 G;  1ZZI A;  4LIJ A;  4WAL A;  3L7Z C;  2CPQ A;  2Z0S A;  2CTM A;  2BA0 A;  2YQR A;  2PQU A;  2P2R A;  4B8T A;  2JZX A;  2CTJ A;  2PY9 A;  2CTL A;  4AM3 A;  4WAN A;  2CTK A;  4JVH A;  1X4M A;  2FMR A;  5JEA G;  1K1G A;  2DGR A;  4OO1 G;  4BA2 I;  1DT4 A;  4QMF B;  3AEV B;  1WE8 A;  2JVZ A;  4JVY A;  5C0X G;  1ZZK A;  2HH2 A;  4AIM A;  4NBQ A;  1WVN 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...

3AEVB

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations