5GAGi

Rnc in complex with srp-sr in the closed state
Total Genus 27

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
27
sequence length
126
structure length
126
Chain Sequence
GFDLNDFLEQLRQMKNMGGXXXXXXXXXXXXXXXXXXXXXXDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKMKKGGXXXXXXXXXXXXXXXXXXX

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.

molecule tags Ribosome
source organism Escherichia coli
publication title Structures of the E. coli translating ribosome with SRP and its receptor and with the translocon.
pubmed doi rcsb
molecule keywords SRP 4.5S RNA
total genus 27
structure length 126
sequence length 126
ec nomenclature
pdb deposition date 2015-11-26

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
i PF00448 SRP54 SRP54-type protein, GTPase domain
i PF02881 SRP54_N SRP54-type protein, helical bundle domain
i PF02978 SRP_SPB Signal peptide binding domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.260.30 Mainly Alpha Orthogonal Bundle 434 Repressor (Amino-terminal Domain) Signal recognition particle, SRP54 subunit, M-domain 5gagi00
2PXLA 2PXPA 2PXQA 2JQEA 2PXTA 3KL4A 2PXUA 1HQ1A 2PXEA 3DM5A 1DULA 2XXAA 2PXBA 1QB2A 2FFHA 5GAHi 2V3CC 2PXDA 3LQXA 3NDBB 2PXVA 2PXFA 1QZXA 5GAGi 1MFQC 2PXKA
chains in the Genus database with same CATH superfamily
1QQAA 2AUWA 4YBAA 2LYSA 2WIUB 5DTQA 2XIUA 3KL4A 2PXTA 3DNVB 2O4AA 1POUA 3F52A 2L1PA 1QB2A 4X4HA 2FFHA 1U2ZA 1UXCA 1CQTA 4X4BA 3GBFA 3KXAA 2BJCA 1OSLA 2WUSR 3PE5A 3F6WA 3BDNA 4IWRA 2R1JL 4JCYA 1JH9A 1Y9QA 2XXAA 3IVPA 3M9LA 4EKGA 2PUDA 4JCXA 1LMB3 2PUBA 1PRVA 5DTRA 2PXVA 1ZUGA 1RIOA 2GRLA 4Z5DA 3GZCA 4HRAA 3QYXA 3S8QA 3HZIB 1ADRA 3OP9A 4Z58A 1NERA 1PRAA 2EBYA 2LLWA 4WVLA 1QP4A 3SX0A 3BD1A 5DTMA 1O4XA 1EFAA 2IVBA 2FJRA 1DWKA 5DRTA 2KEJA 2AW6A 3R09A 3G5GA 3GZDC 3G7DA 2EWTA 1ZAYA 3VWSA 2AWIA 2CROA 4EQZA 2IVGA 1ZZCA 3JXDL 1XWRA 5DSXA 1HF0A 2KEKA 2PXUA 4YG4A 2HCNA 3BS3A 3QOXA 4NDWA 2LYJA 3QQ6A 1QQBA 1X57A 3NDBB 3SR4A 1S7EA 3G0TA 3ZKCA 5GAGi 2MEZA 4MCXA 3MLFA 4PU8A 4F8DA 2XI8A 2O38A 1PNRA 3OWQA 1RZRD 5DT2A 2IUOA 4I6RA 4X4EA 3LQXA 4ER3A 2LCVA 1X2LA 4YARA 4DE9A 2IU7A 2PUAA 3TFLA 2LYQA 1DW9A 1LLIA 3QFIA 3KJXA 3PXPA 4X4CA 2LNMA 2VEOA 1WETA 3LISA 2LYKA 2J7UA 4I6UA 2AXUA 4YG1A 5GAHi 2PXDA 4Y42A 3EUSA 1UTXA 4EZIA 3SCGA 4Q2JA 3OQMA 3FYMA 1BDIA 4O8BA 1CJGA 3RZZA 2L49A 2HINA 3TELA 4OBMA 3OKZA 4X4FA 3NXHA 3H5TA 1WH6A 3FMYA 2R63A 1QZXA 2OR1L 3TEPA 2H8RA 4ER0A 3OMTA 1E3OC 5DRYA 2BNMA 4I6TA 3CLCA 4IVZA 3SCHA 1DULA 3A9XA 1VPWA 4Z5CA 2PPXA 1LQCA 4X4DA 1L1MA 1R63A 2AXZA 2V3CC 2O49A 1QP7A 3VK0A 1ZZ8A 4J1WA 3ZHMA 4OB4A 2PXQA 1JFTA 4EKIA 1HQ1A 1LCDA 1ZZ9A 4YG7B 2A6CA 2EF8A 2IV1A 2PUGA 4I8TA 3LFPA 2BNNA 4MCTA 1ZS4A 2BNOA 3OQNA 2PUCA 2PXFA 3F51A 3FYAA 3GZDA 2PXLA 2HFZA 4EK9A 2J7WA 1R69A 1LCCA 3DM5A 4DE8A 2XJ3A 4ER6A 3UFDA 2PE5A 1AU7A 1OCTC 3ME5A 4GQMA 1ZZ6A 2PXKA 1Y7YA 2YBDA 2LYLA 4GHJA 2PUFA 1ZZBA 3B7HA 2M4HA 3R1FA 3CECA 1GT0C 5A7LA 4X4IA 4IA8A 4J1XA 4Z5HA 3ZHIA 2KEIA 1PRUA 4FN3A 3O9XA 1RZRA 2L8NA 1ZPQA 1BDHA 1PERL 3OQOA 3GN5A 2GZUA 3GN5B 2PXBA 2GRMA 1SQ8A 1QP0A 2CSFA 2ICTA 4ER5A 2JCGA 1IC8A 1B0NA 3A9ZA 2ODRD 2KPJA 4FBIA 4PU4C 1ZZ7A 2XSDC 1UXDA 1QPZA 2JVLA 1YSEA 2AXVA 3NZLA 2HCSA 2ICPA 4PU3C 3NROA 5K98B 2B5AA 1ZVVA 2PIJA 2MXDA 2HSGA 1WIZA 2PUEA 2JQEA 2XXQA 2KZ8A 3SCFA 1JWLA 4JQDA 4Z59A 2PXEA 3UWPA 5JUWA 2XCJA 2OFYA 3TRBA 1NEQA 3L1PA 1RZSA 1RPEL 2XXPA 3A9YA 1NW3A 1MFQC 3JXCL 2PXPA 2LYPA 2LYRA 4X4GA 1JFSA 3MEJA 2MQKA 3QF3A 3D1NI 2IVQA 4PU7A 3JXBC 1WH8A 3KZ3A 4ER7A 3CROL 3ZPXA 3QWGA 3GUUA 3U3WA 3QOWA 2LLVA 2D5VA
chains in the Genus database with same CATH topology
2PXLA 2PXPA 2PXQA 2JQEA 2PXTA 3KL4A 2PXUA 1HQ1A 2PXEA 3DM5A 1DULA 2XXAA 2PXBA 1QB2A 2FFHA 5GAHi 2V3CC 2PXDA 3LQXA 3NDBB 2PXVA 2PXFA 1QZXA 5GAGi 1MFQC 2PXKA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2PXL A;  2PXP A;  2PXQ A;  2JQE A;  2PXT A;  3KL4 A;  2PXU A;  1HQ1 A;  2PXE A;  3DM5 A;  1DUL A;  2XXA A;  2PXB A;  1QB2 A;  2FFH A;  5GAH i;  2V3C C;  2PXD A;  3LQX A;  3NDB B;  2PXV A;  2PXF A;  1QZX A;  5GAG i;  1MFQ C;  2PXK A; 
#chains in the Genus database with same CATH topology
 1QQA A;  2AUW A;  4YBA A;  2LYS A;  2WIU B;  5DTQ A;  2XIU A;  3KL4 A;  2PXT A;  3DNV B;  2O4A A;  1POU A;  3F52 A;  2L1P A;  1QB2 A;  4X4H A;  2FFH A;  1U2Z A;  1UXC A;  1CQT A;  4X4B A;  3GBF A;  3KXA A;  2BJC A;  1OSL A;  2WUS R;  3PE5 A;  3F6W A;  3BDN A;  4IWR A;  2R1J L;  4JCY A;  1JH9 A;  1Y9Q A;  2XXA A;  3IVP A;  3M9L A;  4EKG A;  2PUD A;  4JCX A;  1LMB 3;  2PUB A;  1PRV A;  5DTR A;  2PXV A;  1ZUG A;  1RIO A;  2GRL A;  4Z5D A;  3GZC A;  4HRA A;  3QYX A;  3S8Q A;  3HZI B;  1ADR A;  3OP9 A;  4Z58 A;  1NER A;  1PRA A;  2EBY A;  2LLW A;  4WVL A;  1QP4 A;  3SX0 A;  3BD1 A;  5DTM A;  1O4X A;  1EFA A;  2IVB A;  2FJR A;  1DWK A;  5DRT A;  2KEJ A;  2AW6 A;  3R09 A;  3G5G A;  3GZD C;  3G7D A;  2EWT A;  1ZAY A;  3VWS A;  2AWI A;  2CRO A;  4EQZ A;  2IVG A;  1ZZC A;  3JXD L;  1XWR A;  5DSX A;  1HF0 A;  2KEK A;  2PXU A;  4YG4 A;  2HCN A;  3BS3 A;  3QOX A;  4NDW A;  2LYJ A;  3QQ6 A;  1QQB A;  1X57 A;  3NDB B;  3SR4 A;  1S7E A;  3G0T A;  3ZKC A;  5GAG i;  2MEZ A;  4MCX A;  3MLF A;  4PU8 A;  4F8D A;  2XI8 A;  2O38 A;  1PNR A;  3OWQ A;  1RZR D;  5DT2 A;  2IUO A;  4I6R A;  4X4E A;  3LQX A;  4ER3 A;  2LCV A;  1X2L A;  4YAR A;  4DE9 A;  2IU7 A;  2PUA A;  3TFL A;  2LYQ A;  1DW9 A;  1LLI A;  3QFI A;  3KJX A;  3PXP A;  4X4C A;  2LNM A;  2VEO A;  1WET A;  3LIS A;  2LYK A;  2J7U A;  4I6U A;  2AXU A;  4YG1 A;  5GAH i;  2PXD A;  4Y42 A;  3EUS A;  1UTX A;  4EZI A;  3SCG A;  4Q2J A;  3OQM A;  3FYM A;  1BDI A;  4O8B A;  1CJG A;  3RZZ A;  2L49 A;  2HIN A;  3TEL A;  4OBM A;  3OKZ A;  4X4F A;  3NXH A;  3H5T A;  1WH6 A;  3FMY A;  2R63 A;  1QZX A;  2OR1 L;  3TEP A;  2H8R A;  4ER0 A;  3OMT A;  1E3O C;  5DRY A;  2BNM A;  4I6T A;  3CLC A;  4IVZ A;  3SCH A;  1DUL A;  3A9X A;  1VPW A;  4Z5C A;  2PPX A;  1LQC A;  4X4D A;  1L1M A;  1R63 A;  2AXZ A;  2V3C C;  2O49 A;  1QP7 A;  3VK0 A;  1ZZ8 A;  4J1W A;  3ZHM A;  4OB4 A;  2PXQ A;  1JFT A;  4EKI A;  1HQ1 A;  1LCD A;  1ZZ9 A;  4YG7 B;  2A6C A;  2EF8 A;  2IV1 A;  2PUG A;  4I8T A;  3LFP A;  2BNN A;  4MCT A;  1ZS4 A;  2BNO A;  3OQN A;  2PUC A;  2PXF A;  3F51 A;  3FYA A;  3GZD A;  2PXL A;  2HFZ A;  4EK9 A;  2J7W A;  1R69 A;  1LCC A;  3DM5 A;  4DE8 A;  2XJ3 A;  4ER6 A;  3UFD A;  2PE5 A;  1AU7 A;  1OCT C;  3ME5 A;  4GQM A;  1ZZ6 A;  2PXK A;  1Y7Y A;  2YBD A;  2LYL A;  4GHJ A;  2PUF A;  1ZZB A;  3B7H A;  2M4H A;  3R1F A;  3CEC A;  1GT0 C;  5A7L A;  4X4I A;  4IA8 A;  4J1X A;  4Z5H A;  3ZHI A;  2KEI A;  1PRU A;  4FN3 A;  3O9X A;  1RZR A;  2L8N A;  1ZPQ A;  1BDH A;  1PER L;  3OQO A;  3GN5 A;  2GZU A;  3GN5 B;  2PXB A;  2GRM A;  1SQ8 A;  1QP0 A;  2CSF A;  2ICT A;  4ER5 A;  2JCG A;  1IC8 A;  1B0N A;  3A9Z A;  2ODR D;  2KPJ A;  4FBI A;  4PU4 C;  1ZZ7 A;  2XSD C;  1UXD A;  1QPZ A;  2JVL A;  1YSE A;  2AXV A;  3NZL A;  2HCS A;  2ICP A;  4PU3 C;  3NRO A;  5K98 B;  2B5A A;  1ZVV A;  2PIJ A;  2MXD A;  2HSG A;  1WIZ A;  2PUE A;  2JQE A;  2XXQ A;  2KZ8 A;  3SCF A;  1JWL A;  4JQD A;  4Z59 A;  2PXE A;  3UWP A;  5JUW A;  2XCJ A;  2OFY A;  3TRB A;  1NEQ A;  3L1P A;  1RZS A;  1RPE L;  2XXP A;  3A9Y A;  1NW3 A;  1MFQ C;  3JXC L;  2PXP A;  2LYP A;  2LYR A;  4X4G A;  1JFS A;  3MEJ A;  2MQK A;  3QF3 A;  3D1N I;  2IVQ A;  4PU7 A;  3JXB C;  1WH8 A;  3KZ3 A;  4ER7 A;  3CRO L;  3ZPX A;  3QWG A;  3GUU A;  3U3W A;  3QOW A;  2LLV A;  2D5V A; 
#chains in the Genus database with same CATH homology
 2PXL A;  2PXP A;  2PXQ A;  2JQE A;  2PXT A;  3KL4 A;  2PXU A;  1HQ1 A;  2PXE A;  3DM5 A;  1DUL A;  2XXA A;  2PXB A;  1QB2 A;  2FFH A;  5GAH i;  2V3C C;  2PXD A;  3LQX A;  3NDB B;  2PXV A;  2PXF A;  1QZX A;  5GAG i;  1MFQ C;  2PXK A; 
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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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