3DH3 | Genus

Total Genus 60

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	60
sequence length	240
structure length	240
Chain Sequence	DSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRATIGDQVKPGDVVKVNGQLIEPREAEDLVLIALNKPVGIVSTTEDGERDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTKKCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEV

Loading diagram...

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__19281384403978974__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jmolApplet0__19281384403978974__)

vwrOptions:

{ "name":"jmolApplet0","applet":true,"documentBase":"https://genus.fuw.edu.pl/view/3DH3/A/","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__19281384403978974__","codePath":"https:/static/js/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"19281384403978974","bgcolor":"white" }

setting document base to "https://genus.fuw.edu.pl/view/3DH3/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__19281384403978974__ ready

script 1 started

platformSpeed = 8

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	Isomerase/rna
source organism	Escherichia coli
publication title	Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome. pubmed doi rcsb
molecule keywords	Ribosomal large subunit pseudouridine synthase F
total genus	60
structure length	240
sequence length	240
chains with identical sequence	B, C, D
ec nomenclature	ec 5.4.99.21: 23S rRNA pseudouridine(2604) synthase.
pdb deposition date	2008-06-16

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
A	PF00849	PseudoU_synth_2	RNA pseudouridylate synthase
A	PF01479	S4	S4 domain

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

cath code	Class	Architecture	Topology	Homology	Domain
3.10.290.10	Alpha Beta	Roll	Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A	RNA-binding S4 domain	3dh3A01
3.30.2350.10	Alpha Beta	2-Layer Sandwich	Pseudouridine synthase	Pseudouridine synthase	3dh3A02

3LWVA 1HR0D 2UUBD 2HHHD 1P9KA 2ZM6D 2KTLA 1IBKD 2ISTA 4DV1D 4AQYD 1N32D 3HJYA 4X65D 1HNZD 1IBLD 4LF9D 5BR8D 1XPIA 4JI0D 1PRZA 4LF8D 4B3RD 1R3FA 3T1HD 3T1YD 1HNWD 4JV5D 2UXBD 4JYAD 1H3FA 4DR4D 5IWAD 4DV7D 1I94D 4LGTA 4LFBD 1N36D 4B3TD 1XMQD 1QYUA 2UXDD 4JI2D 2UUAD 4K0KD 5LMND 1IBMD 2VQED 4DV2D 4DV5D 1DM9A 2HVYA 3HP7A 3UAIA 4GKJD 4JI5D 2RFKA 4NXND 1KSLA 4DUZD 3DH3A 4LFCD 2AB4A 1XMOD 4B3SD 1JH3A 1ZL3A 1V9FA 4JI4D 1ZE2A 2AUSA 3HJWA 3LWRA 2JANA 4JI7D 1FJGD 4DR5D 1R3EA 4LF4D 1SGVA 2EY4A 4OUDA 2UXCD 1KSVA 1HNXD 4LFAD 4DV0D 2APOA 2UUCD 4KHPD 1V9KA 4LF6D 3HAXA 4YY3D 4JI6D 4X64D 4DR3D 1C05A 4DUYD 3MQKA 4LABA 4DV3D 4B3MD 4YHHD 3LWOA 3LWQA 1N34D 4DR1D 4DV4D 4X62D 4DR6D 1KSKA 1C06A 4DR7D 4GKKD 4JI1D 2I82A 1K8WA 4X66D 2VQFD 2K6PA 1H3EA 3LWPA 3KBGA 1J5ED 4JI3D 2UU9D 4LF5D 3OTOD 1VIOA 1XNQD 1ZE1A 1XNRD 2E5LD 4OX9D 3U28A 1FKAD 1N33D 4JI8D 4LF7D 2F4VD 4DR2D 4DV6D 4NXMD 5LMUD
chains in the Genus database with same CATH superfamily

3LWVA 1HR0D 2UUBD 2HHHD 3J80E 1P9KA 2ZM6D 2KTLA 1IBKD 2ISTA 4DV1D 4AQYD 1N32D 3HJYA 4X65D 1HNZD 1IBLD 1SB7A 3J81E 4LF9D 5BR8D 1XPIA 5A2QE 4JI0D 3KYDB 1PRZA 4LF8D 4B3RD 5LL6S 1R3FA 1Y8RB 3T1HD 3T1YD 1HNWD 4JV5D 2ZTBA 2UXBD 4JYAD 1H3FA 4DR4D 5IWAD 4DV7D 1I94D 4LGTA 4LFBD 1N36D 4B3TD 1XMQD 1QYUA 2UXDD 1SZWA 4JI2D 2UUAD 1SI7A 4K0KD 2NVUB 5LMND 1IBMD 2VQED 4DV2D 4DV5D 1DM9A 5KNLA 2HVYA 3HP7A 3UAIA 4II2A 3JAME 4GKJD 4JI5D 2RFKA 4NXND 1KSLA 4DUZD 3DH3A 4LFCD 2AB4A 1XMOD 4B3SD 1JH3A 1ZL3A 1V9FA 5FQ2B 4JI4D 1ZE2A 2AUSA 5IT9E 3FN1A 2JANA 4JI7D 3LWRA 3HJWA 1FJGD 3ONHA 4DR5D 2I1SA 1R3EA 4LF4D 1SGVA 2EY4A 4OUDA 2UXCD 1KSVA 1HNXD 4LFAD 4DV0D 2APOA 2UUCD 4KHPD 1V9KA 1Z2ZA 4LF6D 3HAXA 4YY3D 1Y8QB 4JI6D 4X64D 4DR3D 1C05A 4DUYD 3MQKA 4LABA 4DV3D 4B3MD 3KYCB 3ONGA 4YHHD 3LWOA 3CMMA 3LWQA 4W5VB 1N34D 4DR1D 4DV4D 4X62D 4DR6D 4II3A 1KSKA 1C06A 4DR7D 4GKKD 4JI1D 2I82A 3J7AF 1K8WA 4X66D 2VQFD 2K6PA 5FLXE 2LQ7A 1H3EA 3LWPA 3KBGA 1J5ED 4JI3D 2UU9D 4LF5D 3OTOD 1VIOA 1XNQD 1ZE1A 4NNJA 1XNRD 2E5LD 4OX9D 3U28A 1FKAD 1N33D 4JI8D 4LF7D 2F4VD 1Y8XB 4DR2D 4DV6D 4NXMD 5LMUD
chains in the Genus database with same CATH topology

3LWVA 1HR0D 2UUBD 2HHHD 1P9KA 2ZM6D 2KTLA 1IBKD 2ISTA 4DV1D 4AQYD 1N32D 3HJYA 4X65D 1HNZD 1IBLD 1SB7A 4LF9D 5BR8D 1XPIA 4JI0D 1PRZA 4LF8D 4B3RD 1R3FA 3T1HD 3T1YD 1HNWD 4JV5D 2UXBD 4JYAD 1H3FA 4DR4D 5IWAD 4DV7D 1I94D 4LGTA 4LFBD 1N36D 4B3TD 1XMQD 1QYUA 2UXDD 1SZWA 4JI2D 2UUAD 1SI7A 4K0KD 5LMND 1IBMD 2VQED 4DV2D 4DV5D 1DM9A 2HVYA 3HP7A 3UAIA 4GKJD 4JI5D 2RFKA 4NXND 1KSLA 4DUZD 3DH3A 4LFCD 2AB4A 1XMOD 4B3SD 1JH3A 1ZL3A 1V9FA 4JI4D 1ZE2A 2AUSA 3HJWA 3LWRA 2JANA 4JI7D 1FJGD 4DR5D 1R3EA 4LF4D 1SGVA 2EY4A 4OUDA 2UXCD 1KSVA 1HNXD 4LFAD 4DV0D 2APOA 2UUCD 4KHPD 1V9KA 1Z2ZA 4LF6D 3HAXA 4YY3D 4JI6D 4X64D 4DR3D 1C05A 4DUYD 3MQKA 4LABA 4DV3D 4B3MD 4YHHD 3LWOA 3LWQA 1N34D 4DR1D 4DV4D 4X62D 4DR6D 1KSKA 1C06A 4DR7D 4GKKD 4JI1D 2I82A 1K8WA 4X66D 2VQFD 2K6PA 1H3EA 3LWPA 3KBGA 1J5ED 4JI3D 2UU9D 4LF5D 3OTOD 1VIOA 1XNQD 1ZE1A 1XNRD 2E5LD 4OX9D 3U28A 1FKAD 1N33D 4JI8D 4LF7D 2F4VD 4DR2D 4DV6D 4NXMD 5LMUD
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 3LWV A;  1HR0 D;  2UUB D;  2HHH D;  1P9K A;  2ZM6 D;  2KTL A;  1IBK D;  2IST A;  4DV1 D;  4AQY D;  1N32 D;  3HJY A;  4X65 D;  1HNZ D;  1IBL D;  4LF9 D;  5BR8 D;  1XPI A;  4JI0 D;  1PRZ A;  4LF8 D;  4B3R D;  1R3F A;  3T1H D;  3T1Y D;  1HNW D;  4JV5 D;  2UXB D;  4JYA D;  1H3F A;  4DR4 D;  5IWA D;  4DV7 D;  1I94 D;  4LGT A;  4LFB D;  1N36 D;  4B3T D;  1XMQ D;  1QYU A;  2UXD D;  4JI2 D;  2UUA D;  4K0K D;  5LMN D;  1IBM D;  2VQE D;  4DV2 D;  4DV5 D;  1DM9 A;  2HVY A;  3HP7 A;  3UAI A;  4GKJ D;  4JI5 D;  2RFK A;  4NXN D;  1KSL A;  4DUZ D;  3DH3 A;  4LFC D;  2AB4 A;  1XMO D;  4B3S D;  1JH3 A;  1ZL3 A;  1V9F A;  4JI4 D;  1ZE2 A;  2AUS A;  3HJW A;  3LWR A;  2JAN A;  4JI7 D;  1FJG D;  4DR5 D;  1R3E A;  4LF4 D;  1SGV A;  2EY4 A;  4OUD A;  2UXC D;  1KSV A;  1HNX D;  4LFA D;  4DV0 D;  2APO A;  2UUC D;  4KHP D;  1V9K A;  4LF6 D;  3HAX A;  4YY3 D;  4JI6 D;  4X64 D;  4DR3 D;  1C05 A;  4DUY D;  3MQK A;  4LAB A;  4DV3 D;  4B3M D;  4YHH D;  3LWO A;  3LWQ A;  1N34 D;  4DR1 D;  4DV4 D;  4X62 D;  4DR6 D;  1KSK A;  1C06 A;  4DR7 D;  4GKK D;  4JI1 D;  2I82 A;  1K8W A;  4X66 D;  2VQF D;  2K6P A;  1H3E A;  3LWP A;  3KBG A;  1J5E D;  4JI3 D;  2UU9 D;  4LF5 D;  3OTO D;  1VIO A;  1XNQ D;  1ZE1 A;  1XNR D;  2E5L D;  4OX9 D;  3U28 A;  1FKA D;  1N33 D;  4JI8 D;  4LF7 D;  2F4V D;  4DR2 D;  4DV6 D;  4NXM D;  5LMU D; 
#chains in the Genus database with same CATH topology
 3LWV A;  1HR0 D;  2UUB D;  2HHH D;  3J80 E;  1P9K A;  2ZM6 D;  2KTL A;  1IBK D;  2IST A;  4DV1 D;  4AQY D;  1N32 D;  3HJY A;  4X65 D;  1HNZ D;  1IBL D;  1SB7 A;  3J81 E;  4LF9 D;  5BR8 D;  1XPI A;  5A2Q E;  4JI0 D;  3KYD B;  1PRZ A;  4LF8 D;  4B3R D;  5LL6 S;  1R3F A;  1Y8R B;  3T1H D;  3T1Y D;  1HNW D;  4JV5 D;  2ZTB A;  2UXB D;  4JYA D;  1H3F A;  4DR4 D;  5IWA D;  4DV7 D;  1I94 D;  4LGT A;  4LFB D;  1N36 D;  4B3T D;  1XMQ D;  1QYU A;  2UXD D;  1SZW A;  4JI2 D;  2UUA D;  1SI7 A;  4K0K D;  2NVU B;  5LMN D;  1IBM D;  2VQE D;  4DV2 D;  4DV5 D;  1DM9 A;  5KNL A;  2HVY A;  3HP7 A;  3UAI A;  4II2 A;  3JAM E;  4GKJ D;  4JI5 D;  2RFK A;  4NXN D;  1KSL A;  4DUZ D;  3DH3 A;  4LFC D;  2AB4 A;  1XMO D;  4B3S D;  1JH3 A;  1ZL3 A;  1V9F A;  5FQ2 B;  4JI4 D;  1ZE2 A;  2AUS A;  5IT9 E;  3FN1 A;  2JAN A;  4JI7 D;  3LWR A;  3HJW A;  1FJG D;  3ONH A;  4DR5 D;  2I1S A;  1R3E A;  4LF4 D;  1SGV A;  2EY4 A;  4OUD A;  2UXC D;  1KSV A;  1HNX D;  4LFA D;  4DV0 D;  2APO A;  2UUC D;  4KHP D;  1V9K A;  1Z2Z A;  4LF6 D;  3HAX A;  4YY3 D;  1Y8Q B;  4JI6 D;  4X64 D;  4DR3 D;  1C05 A;  4DUY D;  3MQK A;  4LAB A;  4DV3 D;  4B3M D;  3KYC B;  3ONG A;  4YHH D;  3LWO A;  3CMM A;  3LWQ A;  4W5V B;  1N34 D;  4DR1 D;  4DV4 D;  4X62 D;  4DR6 D;  4II3 A;  1KSK A;  1C06 A;  4DR7 D;  4GKK D;  4JI1 D;  2I82 A;  3J7A F;  1K8W A;  4X66 D;  2VQF D;  2K6P A;  5FLX E;  2LQ7 A;  1H3E A;  3LWP A;  3KBG A;  1J5E D;  4JI3 D;  2UU9 D;  4LF5 D;  3OTO D;  1VIO A;  1XNQ D;  1ZE1 A;  4NNJ A;  1XNR D;  2E5L D;  4OX9 D;  3U28 A;  1FKA D;  1N33 D;  4JI8 D;  4LF7 D;  2F4V D;  1Y8X B;  4DR2 D;  4DV6 D;  4NXM D;  5LMU D; 
#chains in the Genus database with same CATH homology
 3LWV A;  1HR0 D;  2UUB D;  2HHH D;  1P9K A;  2ZM6 D;  2KTL A;  1IBK D;  2IST A;  4DV1 D;  4AQY D;  1N32 D;  3HJY A;  4X65 D;  1HNZ D;  1IBL D;  1SB7 A;  4LF9 D;  5BR8 D;  1XPI A;  4JI0 D;  1PRZ A;  4LF8 D;  4B3R D;  1R3F A;  3T1H D;  3T1Y D;  1HNW D;  4JV5 D;  2UXB D;  4JYA D;  1H3F A;  4DR4 D;  5IWA D;  4DV7 D;  1I94 D;  4LGT A;  4LFB D;  1N36 D;  4B3T D;  1XMQ D;  1QYU A;  2UXD D;  1SZW A;  4JI2 D;  2UUA D;  1SI7 A;  4K0K D;  5LMN D;  1IBM D;  2VQE D;  4DV2 D;  4DV5 D;  1DM9 A;  2HVY A;  3HP7 A;  3UAI A;  4GKJ D;  4JI5 D;  2RFK A;  4NXN D;  1KSL A;  4DUZ D;  3DH3 A;  4LFC D;  2AB4 A;  1XMO D;  4B3S D;  1JH3 A;  1ZL3 A;  1V9F A;  4JI4 D;  1ZE2 A;  2AUS A;  3HJW A;  3LWR A;  2JAN A;  4JI7 D;  1FJG D;  4DR5 D;  1R3E A;  4LF4 D;  1SGV A;  2EY4 A;  4OUD A;  2UXC D;  1KSV A;  1HNX D;  4LFA D;  4DV0 D;  2APO A;  2UUC D;  4KHP D;  1V9K A;  1Z2Z A;  4LF6 D;  3HAX A;  4YY3 D;  4JI6 D;  4X64 D;  4DR3 D;  1C05 A;  4DUY D;  3MQK A;  4LAB A;  4DV3 D;  4B3M D;  4YHH D;  3LWO A;  3LWQ A;  1N34 D;  4DR1 D;  4DV4 D;  4X62 D;  4DR6 D;  1KSK A;  1C06 A;  4DR7 D;  4GKK D;  4JI1 D;  2I82 A;  1K8W A;  4X66 D;  2VQF D;  2K6P A;  1H3E A;  3LWP A;  3KBG A;  1J5E D;  4JI3 D;  2UU9 D;  4LF5 D;  3OTO D;  1VIO A;  1XNQ D;  1ZE1 A;  1XNR D;  2E5L D;  4OX9 D;  3U28 A;  1FKA D;  1N33 D;  4JI8 D;  4LF7 D;  2F4V D;  4DR2 D;  4DV6 D;  4NXM D;  5LMU D;

...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...

3DH3A

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations