4PIR | Genus

Total Genus 100

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	100
sequence length	445
structure length	383
Chain Sequence	TQPALLRLSDHLLANYKKGVRPVRDWRKPTTVSIDVIMYAILNVDEKNQVLTTYIWYRQYWTDEFLQWTPEDFDNVTKLSIPTDSIWVPDILINEFVDVGKSPNIPYVYVHHRGEVQNYKPLQLVTACSLDIYNFPFDVQNCSLTFTSWLHTIQDINITLWRSPEEVRSDKSIFINQGEWELLEVFPQFKEFSIDISNSYAEMKFYVIIRRRPLFYAVSLLLPSIFLMVVDIVGFCLPPDSGERVSFKITLLLGYSVFLIIVSDTLPATPLIGVYFVVCMALLVISLAETIFIVRLVHKQDLQRPVPDWLRHLVLDRIAWILCVRGLLQELSSIRHFLEKRDEMREVARDWLRVGYVLDRLLFRIYLLAVLAYSITLVTLWSI

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__410775451672441__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__410775451672441__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/4PIR/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__410775451672441__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"410775451672441","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/4PIR/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__410775451672441__ ready

script 1 started

platformSpeed = 8

Viewer cachePut cache://localLOAD_/file/5d0092bd1bf47761a70594f9/pdb.gz

Viewer cachePut https://genus.fuw.edu.pl/file/5d0092bd1bf47761a70594f9/pdb.gz

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	Transport protein
source organism	Mus musculus
publication title	X-ray structure of the mouse serotonin 5-HT3 receptor. pubmed doi rcsb
molecule keywords	5-hydroxytryptamine receptor 3A
total genus	100
structure length	383
sequence length	445
chains with identical sequence	B, C, D, E
ec nomenclature
pdb deposition date	2014-05-09

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF02931	Neur_chan_LBD	Neurotransmitter-gated ion-channel ligand binding domain
A	PF02932	Neur_chan_memb	Neurotransmitter-gated ion-channel transmembrane region

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

cath code	Class	Architecture	Topology	Homology	Domain
2.70.170.10	Mainly Beta	Distorted Sandwich	Acetylcholine Binding Protein; Chain: A,	Neurotransmitter-gated ion-channel ligand-binding domain	4pirA01

5BP0A 2XQ4A 2BYQA 4IREA 4ZZCA 4LMLA 4NPPA 5FJVA 5AFJA 2XNTA 2XQ7A 2YKSA 3RQUA 4ZJTA 3WIPA 4F8HA 2BYRA 5AINA 5IUXA 3UU5A 1UW6A 4HFHA 5AFLA 3UUBA 4FRRA 2WZYA 3P50A 4AFTA 4Z90A 5HEJA 4QACA 3U8MA 3ZDHA 5KZUA 2XQ9A 4ZRUA 3SH1A 4IL4A 5HEUA 3WTNA 3SQ9A 2WNCA 2VL0A 5HCJA 2C9TA 4COFA 4HFIA 4UY2A 5AFMA 3JAFA 3WTHA 4DBMA 2YOEA 3ZDGA 4B5DA 3RQWA 4HFDA 2XZ5A 2BYPA 2QC1B 3UU6A 3SIOA 5J5HA 4A98A 4IL9A 3RHWA 2YMEA 4ILCA 4WV9A 4AFGA 4TNWA 5J5FA 2BR8A 2W8GA 5AFNA 3SQ6A 3ZKRA 5J5GA 4AFHA 2X00D 4NZBA 4HFEA 3EHZA 3C84A 4Z91A 2Y57A 3TLUA 4LMKA 4XK9A 2PH9A 3RI5A 2Y54A 3UQ4A 3JAEA 1UX2A 2XQ5A 2PGZA 5CO5A 2XZ6A 5HEGA 2BJ0A 2BG9B 3U8LA 5CFBA 2XQAA 2XQ3A 5SYOA 5HCMA 2BR7A 3T4MA 2XQ6A 3GUAA 5J5IA 4QABA 3WTJA 4TWFA 4ZR6A 2WNJA 4HFCA 5BW2A 4LMJA 3TLVA 2ZJVA 2WNLA 4ILBA 3UU3A 2X00A 2Y58A 5JMEA 4HQPA 5BRXA 3WTMA 4TWDA 3C79A 1UV6A 2XYTA 4ZJSA 4D01A 5LXBA 4BFQA 2YN6A 3UQ7A 4PIRA 3UU4A 4UM3S 3U8JA 2XQ8A 5AFMB 2ZJUA 4UM3A 3TLWA 5TVCA 4ZZBA 3PEOA 3EAMA 2BG9A 4ZK4A 3IGQA 4TNVA 4TWHA 4ZK1A 3WTIA 1I9BA 2BYNA 4QH4A 5HEHA 3U8NA 5L47A 4BQTA 3PMZA 2XNUA 3RIFA 5LG3A 2XYSA 4HFBA 5L4EA 4QAAA 2UZ6A 2WN9A 3LSVA 3WTOA 5AFKA 2Y56A 2Y7YA 2XNVA 5HEOA 3P4WA 4UM1A 3WTKA 2BG9C 4UM3P 2YMDA 3TLTA 3RIAA 4A97A 4ALXA 4QH5A 4UXUA 4ILAA 2BG9E 3UU8A 3WTLA 5AFHA 5L4HA 5KE4A 2BYSA 3EI0A 3JADA 4QH1A 4XHEA 3TLSA 4X5TA 2W8FA 4EZ1A 5J0ZA 3U8KA
chains in the Genus database with same CATH superfamily

#chains in the Genus database with same CATH superfamily
 5BP0 A;  2XQ4 A;  2BYQ A;  4IRE A;  4ZZC A;  4LML A;  4NPP A;  5FJV A;  5AFJ A;  2XNT A;  2XQ7 A;  2YKS A;  3RQU A;  4ZJT A;  3WIP A;  4F8H A;  2BYR A;  5AIN A;  5IUX A;  3UU5 A;  1UW6 A;  4HFH A;  5AFL A;  3UUB A;  4FRR A;  2WZY A;  3P50 A;  4AFT A;  4Z90 A;  5HEJ A;  4QAC A;  3U8M A;  3ZDH A;  5KZU A;  2XQ9 A;  4ZRU A;  3SH1 A;  4IL4 A;  5HEU A;  3WTN A;  3SQ9 A;  2WNC A;  2VL0 A;  5HCJ A;  2C9T A;  4COF A;  4HFI A;  4UY2 A;  5AFM A;  3JAF A;  3WTH A;  4DBM A;  2YOE A;  3ZDG A;  4B5D A;  3RQW A;  4HFD A;  2XZ5 A;  2BYP A;  2QC1 B;  3UU6 A;  3SIO A;  5J5H A;  4A98 A;  4IL9 A;  3RHW A;  2YME A;  4ILC A;  4WV9 A;  4AFG A;  4TNW A;  5J5F A;  2BR8 A;  2W8G A;  5AFN A;  3SQ6 A;  3ZKR A;  5J5G A;  4AFH A;  2X00 D;  4NZB A;  4HFE A;  3EHZ A;  3C84 A;  4Z91 A;  2Y57 A;  3TLU A;  4LMK A;  4XK9 A;  2PH9 A;  3RI5 A;  2Y54 A;  3UQ4 A;  3JAE A;  1UX2 A;  2XQ5 A;  2PGZ A;  5CO5 A;  2XZ6 A;  5HEG A;  2BJ0 A;  2BG9 B;  3U8L A;  5CFB A;  2XQA A;  2XQ3 A;  5SYO A;  5HCM A;  2BR7 A;  3T4M A;  2XQ6 A;  3GUA A;  5J5I A;  4QAB A;  3WTJ A;  4TWF A;  4ZR6 A;  2WNJ A;  4HFC A;  5BW2 A;  4LMJ A;  3TLV A;  2ZJV A;  2WNL A;  4ILB A;  3UU3 A;  2X00 A;  2Y58 A;  5JME A;  4HQP A;  5BRX A;  3WTM A;  4TWD A;  3C79 A;  1UV6 A;  2XYT A;  4ZJS A;  4D01 A;  5LXB A;  4BFQ A;  2YN6 A;  3UQ7 A;  4PIR A;  3UU4 A;  4UM3 S;  3U8J A;  2XQ8 A;  5AFM B;  2ZJU A;  4UM3 A;  3TLW A;  5TVC A;  4ZZB A;  3PEO A;  3EAM A;  2BG9 A;  4ZK4 A;  3IGQ A;  4TNV A;  4TWH A;  4ZK1 A;  3WTI A;  1I9B A;  2BYN A;  4QH4 A;  5HEH A;  3U8N A;  5L47 A;  4BQT A;  3PMZ A;  2XNU A;  3RIF A;  5LG3 A;  2XYS A;  4HFB A;  5L4E A;  4QAA A;  2UZ6 A;  2WN9 A;  3LSV A;  3WTO A;  5AFK A;  2Y56 A;  2Y7Y A;  2XNV A;  5HEO A;  3P4W A;  4UM1 A;  3WTK A;  2BG9 C;  4UM3 P;  2YMD A;  3TLT A;  3RIA A;  4A97 A;  4ALX A;  4QH5 A;  4UXU A;  4ILA A;  2BG9 E;  3UU8 A;  3WTL A;  5AFH A;  5L4H A;  5KE4 A;  2BYS A;  3EI0 A;  3JAD A;  4QH1 A;  4XHE A;  3TLS A;  4X5T A;  2W8F A;  4EZ1 A;  5J0Z A;  3U8K A; 
#chains in the Genus database with same CATH topology
 5BP0 A;  2XQ4 A;  2BYQ A;  4IRE A;  4ZZC A;  4LML A;  4NPP A;  5FJV A;  5AFJ A;  2XNT A;  2XQ7 A;  2YKS A;  3RQU A;  4ZJT A;  3WIP A;  4F8H A;  2BYR A;  5AIN A;  5IUX A;  3UU5 A;  1UW6 A;  4HFH A;  5AFL A;  3UUB A;  4FRR A;  2WZY A;  3P50 A;  4AFT A;  4Z90 A;  5HEJ A;  4QAC A;  3U8M A;  3ZDH A;  5KZU A;  2XQ9 A;  4ZRU A;  3SH1 A;  4IL4 A;  5HEU A;  3WTN A;  3SQ9 A;  2WNC A;  2VL0 A;  5HCJ A;  2C9T A;  4COF A;  4HFI A;  4UY2 A;  5AFM A;  3JAF A;  3WTH A;  4DBM A;  2YOE A;  3ZDG A;  4B5D A;  3RQW A;  4HFD A;  2XZ5 A;  2BYP A;  2QC1 B;  3UU6 A;  3SIO A;  5J5H A;  4A98 A;  4IL9 A;  3RHW A;  2YME A;  4ILC A;  4WV9 A;  4AFG A;  4TNW A;  5J5F A;  2BR8 A;  2W8G A;  5AFN A;  3SQ6 A;  3ZKR A;  5J5G A;  4AFH A;  2X00 D;  4NZB A;  4HFE A;  3EHZ A;  3C84 A;  4Z91 A;  2Y57 A;  3TLU A;  4LMK A;  4XK9 A;  2PH9 A;  3RI5 A;  2Y54 A;  3UQ4 A;  3JAE A;  1UX2 A;  2XQ5 A;  2PGZ A;  5CO5 A;  2XZ6 A;  5HEG A;  2BJ0 A;  2BG9 B;  3U8L A;  5CFB A;  2XQA A;  2XQ3 A;  5SYO A;  5HCM A;  2BR7 A;  3T4M A;  2XQ6 A;  3GUA A;  5J5I A;  4QAB A;  3WTJ A;  4TWF A;  4ZR6 A;  2WNJ A;  4HFC A;  5BW2 A;  4LMJ A;  3TLV A;  2ZJV A;  2WNL A;  4ILB A;  3UU3 A;  2X00 A;  2Y58 A;  5JME A;  4HQP A;  5BRX A;  3WTM A;  4TWD A;  3C79 A;  1UV6 A;  2XYT A;  4ZJS A;  4D01 A;  5LXB A;  4BFQ A;  2YN6 A;  3UQ7 A;  4PIR A;  3UU4 A;  4UM3 S;  3U8J A;  2XQ8 A;  5AFM B;  2ZJU A;  4UM3 A;  3TLW A;  5TVC A;  4ZZB A;  3PEO A;  3EAM A;  2BG9 A;  4ZK4 A;  3IGQ A;  4TNV A;  4TWH A;  4ZK1 A;  3WTI A;  1I9B A;  2BYN A;  4QH4 A;  5HEH A;  3U8N A;  5L47 A;  4BQT A;  3PMZ A;  2XNU A;  3RIF A;  5LG3 A;  2XYS A;  4HFB A;  5L4E A;  4QAA A;  2UZ6 A;  2WN9 A;  3LSV A;  3WTO A;  5AFK A;  2Y56 A;  2Y7Y A;  2XNV A;  5HEO A;  3P4W A;  4UM1 A;  3WTK A;  2BG9 C;  4UM3 P;  2YMD A;  3TLT A;  3RIA A;  4A97 A;  4ALX A;  4QH5 A;  4UXU A;  4ILA A;  2BG9 E;  3UU8 A;  3WTL A;  5AFH A;  5L4H A;  5KE4 A;  2BYS A;  3EI0 A;  3JAD A;  4QH1 A;  4XHE A;  3TLS A;  4X5T A;  2W8F A;  4EZ1 A;  5J0Z A;  3U8K A; 
#chains in the Genus database with same CATH homology
 5BP0 A;  2XQ4 A;  2BYQ A;  4IRE A;  4ZZC A;  4LML A;  4NPP A;  5FJV A;  5AFJ A;  2XNT A;  2XQ7 A;  2YKS A;  3RQU A;  4ZJT A;  3WIP A;  4F8H A;  2BYR A;  5AIN A;  5IUX A;  3UU5 A;  1UW6 A;  4HFH A;  5AFL A;  3UUB A;  4FRR A;  2WZY A;  3P50 A;  4AFT A;  4Z90 A;  5HEJ A;  4QAC A;  3U8M A;  3ZDH A;  5KZU A;  2XQ9 A;  4ZRU A;  3SH1 A;  4IL4 A;  5HEU A;  3WTN A;  3SQ9 A;  2WNC A;  2VL0 A;  5HCJ A;  2C9T A;  4COF A;  4HFI A;  4UY2 A;  5AFM A;  3JAF A;  3WTH A;  4DBM A;  2YOE A;  3ZDG A;  4B5D A;  3RQW A;  4HFD A;  2XZ5 A;  2BYP A;  2QC1 B;  3UU6 A;  3SIO A;  5J5H A;  4A98 A;  4IL9 A;  3RHW A;  2YME A;  4ILC A;  4WV9 A;  4AFG A;  4TNW A;  5J5F A;  2BR8 A;  2W8G A;  5AFN A;  3SQ6 A;  3ZKR A;  5J5G A;  4AFH A;  2X00 D;  4NZB A;  4HFE A;  3EHZ A;  3C84 A;  4Z91 A;  2Y57 A;  3TLU A;  4LMK A;  4XK9 A;  2PH9 A;  3RI5 A;  2Y54 A;  3UQ4 A;  3JAE A;  1UX2 A;  2XQ5 A;  2PGZ A;  5CO5 A;  2XZ6 A;  5HEG A;  2BJ0 A;  2BG9 B;  3U8L A;  5CFB A;  2XQA A;  2XQ3 A;  5SYO A;  5HCM A;  2BR7 A;  3T4M A;  2XQ6 A;  3GUA A;  5J5I A;  4QAB A;  3WTJ A;  4TWF A;  4ZR6 A;  2WNJ A;  4HFC A;  5BW2 A;  4LMJ A;  3TLV A;  2ZJV A;  2WNL A;  4ILB A;  3UU3 A;  2X00 A;  2Y58 A;  5JME A;  4HQP A;  5BRX A;  3WTM A;  4TWD A;  3C79 A;  1UV6 A;  2XYT A;  4ZJS A;  4D01 A;  5LXB A;  4BFQ A;  2YN6 A;  3UQ7 A;  4PIR A;  3UU4 A;  4UM3 S;  3U8J A;  2XQ8 A;  5AFM B;  2ZJU A;  4UM3 A;  3TLW A;  5TVC A;  4ZZB A;  3PEO A;  3EAM A;  2BG9 A;  4ZK4 A;  3IGQ A;  4TNV A;  4TWH A;  4ZK1 A;  3WTI A;  1I9B A;  2BYN A;  4QH4 A;  5HEH A;  3U8N A;  5L47 A;  4BQT A;  3PMZ A;  2XNU A;  3RIF A;  5LG3 A;  2XYS A;  4HFB A;  5L4E A;  4QAA A;  2UZ6 A;  2WN9 A;  3LSV A;  3WTO A;  5AFK A;  2Y56 A;  2Y7Y A;  2XNV A;  5HEO A;  3P4W A;  4UM1 A;  3WTK A;  2BG9 C;  4UM3 P;  2YMD A;  3TLT A;  3RIA A;  4A97 A;  4ALX A;  4QH5 A;  4UXU A;  4ILA A;  2BG9 E;  3UU8 A;  3WTL A;  5AFH A;  5L4H A;  5KE4 A;  2BYS A;  3EI0 A;  3JAD A;  4QH1 A;  4XHE A;  3TLS A;  4X5T A;  2W8F A;  4EZ1 A;  5J0Z A;  3U8K 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...

4PIRA

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations