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


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

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