4X64 | Genus

Total Genus 55

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	55
sequence length	208
structure length	208
Chain Sequence	GRYIGPVCRLCRREGVKLYLKGERCYSPKCAMERRPYPPGQHGQKRARRPSDYAVRLREKQKLRRIYGISERQFRNLFEEASKKKGVTGSVFLGLLESRLDNVVYRLGFAVSRRQARQLVRHGHITVNGRRVDLPSYRVRPGDEIAVAEKSRNLELIRQNLEAMKGRKVGPWLSLDVEGMKGKFLRLPDREDLALPVNEQLVIEFYSR

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

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Viewer cachePut cache://localLOAD_/file/5d14454555382acc79ac5a09/pdb.gz

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The Resolver thinks Pdb

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Time for openFile(/file/5d14454555382acc79ac5a09/pdb.gz): 1518 ms

reading 208 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

208 atoms created

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

Time for creating model: 23 ms

Adding embedded #jmolscript: select ({0:207});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

molecule tags	Ribosome/antibiotic
publication title	N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. pubmed doi rcsb
molecule keywords	16S rRNA
total genus	55
structure length	208
sequence length	208
ec nomenclature
pdb deposition date	2014-12-06

pfam database annotations

chain	Pfam Accession Code	Pfam Family Identifier	Pfam Description
D	PF00163	Ribosomal_S4	Ribosomal protein S4/S9 N-terminal domain
D	PF01479	S4	S4 domain

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

cath code	Class	Architecture	Topology	Homology	Domain
1.10.1050.10	Mainly Alpha	Orthogonal Bundle	Ribosomal Protein S4 Delta 41; Chain A, domain 1	Ribosomal Protein S4 Delta 41; Chain A, domain 1	4x64D01
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	4x64D02

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

1IBKD 1J5ED 4JI0D 2K6PA 1JH3A 1IBLD 4LFAD 2UU9D 4DV7D 4NNJA 4II2A 5IT9E 5LL6S 2KTLA 2ZM6D 5LMUD 4JI6D 2LQ7A 5FQ2B 4DUZD 4JYAD 5KNLA 3T1YD 1KSLA 4JI4D 4YY3D 3OTOD 5A2QE 1Y8XB 1H3FA 3HP7A 4X66D 4LF5D 4KHPD 4NXND 1N33D 2UUAD 3ONGA 4DR6D 4JI1D 3J7AF 4JI2D 3KYCB 1C05A 4LF8D 1H3EA 4B3TD 3FN1A 3KYDB 2UUBD 2VQED 3J81E 5IWAD 4DR2D 4LGTA 2VQFD 4LF4D 4LF6D 4DR1D 1XNRD 1KSKA 4DR5D 4DV6D 4AQYD 4LF7D 4DV0D 3J80E 2JANA 1I94D 3CMMA 4JI3D 4YHHD 4DR3D 4B3MD 4JV5D 2ISTA 2ZTBA 5LMND 1N36D 4II3A 1FKAD 1HNXD 5BR8D 2NVUB 5FLXE 4DV1D 4DUYD 1HR0D 4K0KD 3DH3A 1P9KA 4JI8D 4X65D 1XMQD 2L3NA 4LFBD 4JI7D 1HNWD 1FJGD 4NXMD 2F4VD 4X62D 1XNQD 4LFCD 4DR4D 1C06A 4JI5D 3JAME 1KSVA 4B3RD 4W5VB 4DV3D 4X64D 1Y8RB 1XMOD 4B3SD 2HHHD 3T1HD 4DR7D 4OX9D 1VIOA 1Y8QB 3KBGA 2UXDD 1IBMD 4GKKD 2UXBD 2UXCD 2E5LD 4GKJD 1DM9A 4DV2D 4DV4D 3ONHA 2UUCD 1N32D 2I1SA 4OUDA 1HNZD 4DV5D 4LF9D 1N34D
chains in the Genus database with same CATH topology

1IBKD 1J5ED 4JI0D 2K6PA 1JH3A 1IBLD 4LFAD 2UU9D 4DV7D 2KTLA 2ZM6D 5LMUD 4JI6D 4DUZD 4JYAD 3T1YD 1KSLA 4JI4D 4YY3D 3OTOD 1H3FA 3HP7A 4X66D 4LF5D 4KHPD 4NXND 1N33D 2UUAD 4DR6D 4JI1D 4JI2D 1C05A 4LF8D 1H3EA 4B3TD 2UUBD 2VQED 5IWAD 4DR2D 4LGTA 2VQFD 4LF4D 4LF6D 4DR1D 1XNRD 1KSKA 4DR5D 4DV6D 4AQYD 4LF7D 4DV0D 2JANA 1I94D 4JI3D 4YHHD 4DR3D 4B3MD 4JV5D 2ISTA 5LMND 1N36D 1FKAD 1HNXD 5BR8D 4DV1D 4DUYD 1HR0D 4K0KD 3DH3A 1P9KA 4JI8D 4X65D 1XMQD 2L3NA 4LFBD 4JI7D 1HNWD 1FJGD 4NXMD 2F4VD 4X62D 1XNQD 4LFCD 4DR4D 1C06A 4JI5D 1KSVA 4B3RD 4DV3D 4X64D 1XMOD 4B3SD 2HHHD 3T1HD 4DR7D 4OX9D 1VIOA 3KBGA 2UXDD 1IBMD 4GKKD 2UXBD 2UXCD 2E5LD 4GKJD 1DM9A 4DV2D 4DV4D 2UUCD 1N32D 4OUDA 1HNZD 4DV5D 4LF9D 1N34D
chains in the Genus database with same CATH homology

#chains in the Genus database with same CATH superfamily
 1IBK D;  1J5E D;  4JI0 D;  2K6P A;  1JH3 A;  1IBL D;  4LFA D;  2UU9 D;  4DV7 D;  2KTL A;  2ZM6 D;  5LMU D;  4JI6 D;  4DUZ D;  4JYA D;  3T1Y D;  1KSL A;  4JI4 D;  4YY3 D;  3OTO D;  1H3F A;  3HP7 A;  4X66 D;  4LF5 D;  4KHP D;  4NXN D;  1N33 D;  2UUA D;  4DR6 D;  4JI1 D;  4JI2 D;  1C05 A;  4LF8 D;  1H3E A;  4B3T D;  2UUB D;  2VQE D;  5IWA D;  4DR2 D;  4LGT A;  2VQF D;  4LF4 D;  4LF6 D;  4DR1 D;  1XNR D;  1KSK A;  4DR5 D;  4DV6 D;  4AQY D;  4LF7 D;  4DV0 D;  2JAN A;  1I94 D;  4JI3 D;  4YHH D;  4DR3 D;  4B3M D;  4JV5 D;  2IST A;  5LMN D;  1N36 D;  1FKA D;  1HNX D;  5BR8 D;  4DV1 D;  4DUY D;  1HR0 D;  4K0K D;  3DH3 A;  1P9K A;  4JI8 D;  4X65 D;  1XMQ D;  4LFB D;  4JI7 D;  1HNW D;  1FJG D;  4NXM D;  2F4V D;  4X62 D;  1XNQ D;  4LFC D;  4DR4 D;  1C06 A;  4JI5 D;  1KSV A;  4B3R D;  4DV3 D;  4X64 D;  1XMO D;  4B3S D;  2HHH D;  3T1H D;  4DR7 D;  4OX9 D;  1VIO A;  3KBG A;  2UXD D;  1IBM D;  4GKK D;  2UXB D;  2UXC D;  2E5L D;  4GKJ D;  1DM9 A;  4DV2 D;  4DV4 D;  2UUC D;  1N32 D;  4OUD A;  1HNZ D;  4DV5 D;  4LF9 D;  1N34 D; 
#chains in the Genus database with same CATH topology
 1IBK D;  1J5E D;  4JI0 D;  2K6P A;  1JH3 A;  1IBL D;  4LFA D;  2UU9 D;  4DV7 D;  4NNJ A;  4II2 A;  5IT9 E;  5LL6 S;  2KTL A;  2ZM6 D;  5LMU D;  4JI6 D;  2LQ7 A;  5FQ2 B;  4DUZ D;  4JYA D;  5KNL A;  3T1Y D;  1KSL A;  4JI4 D;  4YY3 D;  3OTO D;  5A2Q E;  1Y8X B;  1H3F A;  3HP7 A;  4X66 D;  4LF5 D;  4KHP D;  4NXN D;  1N33 D;  2UUA D;  3ONG A;  4DR6 D;  4JI1 D;  3J7A F;  4JI2 D;  3KYC B;  1C05 A;  4LF8 D;  1H3E A;  4B3T D;  3FN1 A;  3KYD B;  2UUB D;  2VQE D;  3J81 E;  5IWA D;  4DR2 D;  4LGT A;  2VQF D;  4LF4 D;  4LF6 D;  4DR1 D;  1XNR D;  1KSK A;  4DR5 D;  4DV6 D;  4AQY D;  4LF7 D;  4DV0 D;  3J80 E;  2JAN A;  1I94 D;  3CMM A;  4JI3 D;  4YHH D;  4DR3 D;  4B3M D;  4JV5 D;  2IST A;  2ZTB A;  5LMN D;  1N36 D;  4II3 A;  1FKA D;  1HNX D;  5BR8 D;  2NVU B;  5FLX E;  4DV1 D;  4DUY D;  1HR0 D;  4K0K D;  3DH3 A;  1P9K A;  4JI8 D;  4X65 D;  1XMQ D;  2L3N A;  4LFB D;  4JI7 D;  1HNW D;  1FJG D;  4NXM D;  2F4V D;  4X62 D;  1XNQ D;  4LFC D;  4DR4 D;  1C06 A;  4JI5 D;  3JAM E;  1KSV A;  4B3R D;  4W5V B;  4DV3 D;  4X64 D;  1Y8R B;  1XMO D;  4B3S D;  2HHH D;  3T1H D;  4DR7 D;  4OX9 D;  1VIO A;  1Y8Q B;  3KBG A;  2UXD D;  1IBM D;  4GKK D;  2UXB D;  2UXC D;  2E5L D;  4GKJ D;  1DM9 A;  4DV2 D;  4DV4 D;  3ONH A;  2UUC D;  1N32 D;  2I1S A;  4OUD A;  1HNZ D;  4DV5 D;  4LF9 D;  1N34 D; 
#chains in the Genus database with same CATH homology
 1IBK D;  1J5E D;  4JI0 D;  2K6P A;  1JH3 A;  1IBL D;  4LFA D;  2UU9 D;  4DV7 D;  2KTL A;  2ZM6 D;  5LMU D;  4JI6 D;  4DUZ D;  4JYA D;  3T1Y D;  1KSL A;  4JI4 D;  4YY3 D;  3OTO D;  1H3F A;  3HP7 A;  4X66 D;  4LF5 D;  4KHP D;  4NXN D;  1N33 D;  2UUA D;  4DR6 D;  4JI1 D;  4JI2 D;  1C05 A;  4LF8 D;  1H3E A;  4B3T D;  2UUB D;  2VQE D;  5IWA D;  4DR2 D;  4LGT A;  2VQF D;  4LF4 D;  4LF6 D;  4DR1 D;  1XNR D;  1KSK A;  4DR5 D;  4DV6 D;  4AQY D;  4LF7 D;  4DV0 D;  2JAN A;  1I94 D;  4JI3 D;  4YHH D;  4DR3 D;  4B3M D;  4JV5 D;  2IST A;  5LMN D;  1N36 D;  1FKA D;  1HNX D;  5BR8 D;  4DV1 D;  4DUY D;  1HR0 D;  4K0K D;  3DH3 A;  1P9K A;  4JI8 D;  4X65 D;  1XMQ D;  2L3N A;  4LFB D;  4JI7 D;  1HNW D;  1FJG D;  4NXM D;  2F4V D;  4X62 D;  1XNQ D;  4LFC D;  4DR4 D;  1C06 A;  4JI5 D;  1KSV A;  4B3R D;  4DV3 D;  4X64 D;  1XMO D;  4B3S D;  2HHH D;  3T1H D;  4DR7 D;  4OX9 D;  1VIO A;  3KBG A;  2UXD D;  1IBM D;  4GKK D;  2UXB D;  2UXC D;  2E5L D;  4GKJ D;  1DM9 A;  4DV2 D;  4DV4 D;  2UUC D;  1N32 D;  4OUD A;  1HNZ D;  4DV5 D;  4LF9 D;  1N34 D;

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similar chains in the Genus database (?% sequence similarity)

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similar chains in the pdb database (?% sequence similarity)

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#similar chains, but unknotted
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4X64D

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations