5GAGi

Rnc in complex with srp-sr in the closed state
Total Genus 27
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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
27
sequence length
126
structure length
126
Chain Sequence
GFDLNDFLEQLRQMKNMGGXXXXXXXXXXXXXXXXXXXXXXDDKVLVRMEAIINSMTMKERAKPEIIKGSRKRRIAAGCGMQVQDVNRLLKQFDDMQRMMKKMKKGGXXXXXXXXXXXXXXXXXXX
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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.

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


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