1P9KA

The solution structure of ybcj from e. coli reveals a recently discovered alfal motif involved in rna-binding
Total Genus 10
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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
10
sequence length
79
structure length
79
Chain Sequence
GSMIHRMSNMATFSLGKHPHVELCDLLKLEGWSESGAQAKIAIAEGQVKVDGAVETRKRCKIVAGQTVSFAGHSVQVVA
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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

After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Chord Diagram
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molecule keywords orf, hypothetical protein
publication title The solution structure of YbcJ from Escherichia coli reveals a recently discovered alphaL motif involved in RNA binding.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Rna binding protein
total genus 10
structure length 79
sequence length 79
ec nomenclature
pdb deposition date 2003-05-12

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF13275 S4_2 S4 domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
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 1p9kA00
1DM9A 4KHPD 1H3FA 2UUBD 4JI5D 5IWAD 1N36D 2ZM6D 1N32D 4DR5D 4JI4D 4DV7D 4DV0D 2E5LD 4JI8D 2UUAD 2F4VD 4LF8D 4DR1D 1HNWD 3KBGA 2UXDD 1KSLA 4OUDA 1FKAD 1XMQD 4LFCD 1C06A 4DR4D 4DUZD 1HNZD 4DV1D 1IBMD 2VQFD 4NXMD 3T1HD 4LFBD 1P9KA 1IBLD 1FJGD 4B3RD 4DR2D 3T1YD 4JI7D 4DV3D 2UXBD 1KSVA 4JI6D 1KSKA 5LMND 2K6PA 4LF7D 4DV5D 4GKKD 1N33D 4LGTA 2HHHD 4DR6D 2JANA 4JV5D 4DV6D 1HNXD 3HP7A 4DV4D 2UU9D 2ISTA 1N34D 4JI2D 4DV2D 3DH3A 1IBKD 2VQED 1C05A 4B3SD 4LF4D 1H3EA 1JH3A 1XNRD 4X64D 5LMUD 2UUCD 2KTLA 4JI3D 4GKJD 4LF5D 4X65D 1HR0D 4LF9D 4JI1D 2UXCD 4X66D 1J5ED 3OTOD 1I94D 4NXND 4DR7D 4LFAD 1XNQD 4K0KD 4AQYD 4JI0D 1XMOD 4LF6D 4JYAD 4DR3D 4X62D 4YHHD 4OX9D 5BR8D 4DUYD 4B3MD 4B3TD 1VIOA 4YY3D
chains in the Genus database with same CATH superfamily
2LQ7A 1DM9A 1Y8XB 4KHPD 1H3FA 2UUBD 3J7AF 4JI5D 5IWAD 3JAME 1N36D 2ZM6D 1N32D 4DR5D 4JI4D 4DV7D 4DV0D 2E5LD 4JI8D 2UUAD 2F4VD 5A2QE 4NNJA 4LF8D 4DR1D 3ONHA 1HNWD 3KYDB 3KBGA 2UXDD 1KSLA 3FN1A 4II2A 4OUDA 1FKAD 1XMQD 4LFCD 1C06A 4DR4D 4DUZD 1HNZD 4DV1D 1IBMD 2VQFD 4NXMD 3T1HD 3ONGA 4LFBD 1P9KA 1IBLD 1Y8RB 1FJGD 4B3RD 4DR2D 3T1YD 4JI7D 4DV3D 2UXBD 1KSVA 4JI6D 1KSKA 3J81E 2K6PA 5LMND 4LF7D 4DV5D 4GKKD 1N33D 4LGTA 1Y8QB 2HHHD 4DR6D 2JANA 4JV5D 4DV6D 1HNXD 3HP7A 4DV4D 2UU9D 4II3A 2ISTA 1N34D 4JI2D 4DV2D 3DH3A 1IBKD 2VQED 5IT9E 1C05A 4W5VB 4B3SD 4LF4D 3J80E 1H3EA 5FLXE 1JH3A 1XNRD 4X64D 5LMUD 2NVUB 2UUCD 2KTLA 4JI3D 4GKJD 4LF5D 4X65D 1HR0D 4LF9D 4JI1D 2UXCD 4X66D 1J5ED 3OTOD 1I94D 4NXND 4DR7D 4LFAD 2ZTBA 5FQ2B 1XNQD 4K0KD 4AQYD 4JI0D 1XMOD 5KNLA 4LF6D 4JYAD 5LL6S 4DR3D 4X62D 4YHHD 4OX9D 5BR8D 4DUYD 4B3MD 2I1SA 3CMMA 4B3TD 3KYCB 1VIOA 4YY3D
chains in the Genus database with same CATH topology
1DM9A 4KHPD 1H3FA 2UUBD 4JI5D 5IWAD 1N36D 2ZM6D 1N32D 4DR5D 4JI4D 4DV7D 4DV0D 2E5LD 4JI8D 2UUAD 2F4VD 4LF8D 4DR1D 1HNWD 3KBGA 2UXDD 1KSLA 4OUDA 1FKAD 1XMQD 4LFCD 1C06A 4DR4D 4DUZD 1HNZD 4DV1D 1IBMD 2VQFD 4NXMD 3T1HD 4LFBD 1P9KA 1IBLD 1FJGD 4B3RD 4DR2D 3T1YD 4JI7D 4DV3D 2UXBD 1KSVA 4JI6D 1KSKA 5LMND 2K6PA 4LF7D 4DV5D 4GKKD 1N33D 4LGTA 2HHHD 4DR6D 2JANA 4JV5D 4DV6D 1HNXD 3HP7A 4DV4D 2UU9D 2ISTA 1N34D 4JI2D 4DV2D 3DH3A 1IBKD 2VQED 1C05A 4B3SD 4LF4D 1H3EA 1JH3A 1XNRD 4X64D 5LMUD 2UUCD 2KTLA 4JI3D 4GKJD 4LF5D 4X65D 1HR0D 4LF9D 4JI1D 2UXCD 4X66D 1J5ED 3OTOD 1I94D 4NXND 4DR7D 4LFAD 1XNQD 4K0KD 4AQYD 4JI0D 1XMOD 4LF6D 4JYAD 4DR3D 4X62D 4YHHD 4OX9D 5BR8D 4DUYD 4B3MD 4B3TD 1VIOA 4YY3D
chains in the Genus database with same CATH homology


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

 
#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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