5JVGS

The large ribosomal subunit from deinococcus radiodurans in complex with avilamycin
Total Genus 14
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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
14
sequence length
180
structure length
180
Chain Sequence
MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPRLTAEE
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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 tags Ribosome
molecule keywords 23S ribosomal RNA
publication title Avilamycin and evernimicin induce structural changes in rProteins uL16 and CTC that enhance the inhibition of A-site tRNA binding.
pubmed doi rcsb
total genus 14
structure length 180
sequence length 180
ec nomenclature
pdb deposition date 2016-05-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
S PF01386 Ribosomal_L25p Ribosomal L25p family
S PF14693 Ribosomal_TL5_C Ribosomal protein TL5, C-terminal domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.240.10 Mainly Beta Beta Barrel Ribosomal Protein L25; Chain P Ribosomal Protein L25; Chain P 5jvgS01
2.170.120.20 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 Ribosomal protein L25, beta domain 5jvgS02
5IZNA 4WFBS 1EUYA 3AIIA 4IO9S 4WCES 2ZJPS 5GADW 3J7ZV 1EXDA 3CF5S 1QRTA 5DM7S 5GAEW 4JXZA 1FEUA 2HZ7A 3PIOS 1ZJWA 1QRUA 3PIPS 1GTRA 1DFUP 1B75A 1QRSA 5BNZA 4WF9S 5DM6S 2ZJQS 2ZJRS 5GAGW 1O0BA 5GAHW 4WFNS 1D6KA 2RD2A 4IOCS 1O0CA 5HL7S 1EUQA 4UY88 2RE8A 4IOAS 5JVHS 4JXXA 1QTQA 1NYLA 4U67S 3DLLS 4JYZA 4P2BA 4WFAS 1GTSA 5JVGS 4H3SA
chains in the Genus database with same CATH superfamily
2O5JA 2Y0SD 3AIIA 3HOZC 3KW2A 1TWCC 1TWGC 4OIPA 4AYBD 1QRTA 4ZH4A 4LJZA 4A3CC 1FEUA 2NVYC 2A68A 2BE5A 3GTMC 1DFUP 1GTRA 1B75A 3S15C 1QRSA 4V194 2ZJRS 1O0BA 5GAHW 3X1LB 5C44C 4C3JC 3GTKC 3HKZD 4IOCS 4OIRA 3LYWA 1Z85A 5HL7S 1R9TC 3GTLC 3CZBA 5IYCC 5IYDC 4LLGA 1QTQA 1YNJA 1NYLA 3W2WB 4J3CA 4LK0A 2A6EA 4JYZA 4G7HA 2O5IA 4P2BA 4A3LC 4Q5SA 3HOXC 3GTGC 1V6ZA 3EQLA 4KN4A 2PNWA 5JVGS 3WODA 4G7ZA 4OIQA 1QRUA 4H3SA 2B63C 3GTOC 1SMYA 1EUYA 2KPUA 2KQ1A 3I4NC 5TMCA 2ZJPS 4YG2A 4MEYA 2VUMC 5GADW 3J7ZV 4BBSC 2L3UA 4XLPA 3S1RC 4E8BA 3GTQC 2E2IC 3CQZC 4XSZA 2E2JC 4H4KA 4G7OA 2HZ7A 4BY1C 2AE0X 5C4XC 4Y52C 4Q4ZA 2JA6C 2YU9C 4WF9S 1VHKA 4A3DC 2ZJQS 3PO3C 4GZYA 4KMUA 2CW0A 1SFOC 2NVXC 2RD2A 3S1QC 2RE8A 4OINA 2A6HA 2PJJA 4Y7NC 2KXYA 3H3VD 4C3HC 2PICA 4U67S 1TWFC 4C3IC 4NOIA 1I3QC 1HQMA 2PPBA 3GTPC 1GTSA 1WCMC 5IZNA 4WFBS 3H0GC 4A3EC 1NXZA 3S2HC 4IO9S 4A3JC 4X6AC 4XLNA 2JA7C 4QJVA 4YFXA 4JXZA 2NWAA 4BBRC 1Y1WC 3S2DC 3FKIC 4OIOA 4MEXA 4YFKA 1UDXA 5DM6S 4MQ9A 5GAGW 2NVQC 4WFNS 3S16C 5HQHA 4BXXC 1I50C 1EUQA 4UY88 3GTJC 4IOAS 1K83C 2PMZD 3HOYC 4JK1A 5IP9C 3RZDC 3HOUC 4XSXA 1TWHC 3DLLS 1VHYA 4WFAS 3S17C 4A3FC 2EGWA 1I6HC 1YNNA 5IYBC 5C4JC 3HOVC 3M3YC 5C3EC 1BDFA 4A3GC 2R7ZC 4A93C 2EGVA 4WCES 2G6GA 2GAEA 4KN7A 3M4OC 2R93C 5TMFA 1EXDA 2NVTC 4L69A 2PI8A 3CF5S 2R92C 3DXJA 3K7AC 5DM7S 2PA8D 4A3MC 5GAEW 3S1NC 3I4MC 3S1MC 1ZJWA 3PIOS 3PIPS 5D4DA 2G5DA 5BNZA 3PO2C 2L5NA 3S14C 1D6KA 2WAQD 1O0CA 5IP7C 2A69A 2JA5C 2WB1D 2Z0YA 4A3IC 5JVHS 4JXXA 5FLMC 2E2HC 1IW7A 2JA8C 4A3KC 3RZOC 2CX8A 3HOWC 4BY7C 4C2MC 4A3BC 1Y1VC 1I6VA 3W2VB 4LK1A 4YFNA 1ZYRA 1TWAC 4QIWD
chains in the Genus database with same CATH topology
5IZNA 4WFBS 1EUYA 3AIIA 4IO9S 4WCES 2ZJPS 5GADW 3J7ZV 1EXDA 3CF5S 1QRTA 5DM7S 5GAEW 4JXZA 1FEUA 4H4KA 2HZ7A 3PIOS 1ZJWA 1QRUA 3PIPS 1GTRA 1DFUP 1B75A 1QRSA 5BNZA 4WF9S 4V194 5DM6S 1UDXA 2ZJQS 5GAGW 2ZJRS 5GAHW 1O0BA 3X1LB 4WFNS 1D6KA 2RD2A 4IOCS 1O0CA 5HL7S 1EUQA 4UY88 2RE8A 4IOAS 5JVHS 4JXXA 1QTQA 1NYLA 3W2WB 4U67S 3DLLS 4JYZA 4P2BA 4WFAS 3W2VB 1GTSA 5JVGS 4H3SA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 5IZN A;  4WFB S;  1EUY A;  3AII A;  4IO9 S;  4WCE S;  2ZJP S;  5GAD W;  3J7Z V;  1EXD A;  3CF5 S;  1QRT A;  5DM7 S;  5GAE W;  4JXZ A;  1FEU A;  2HZ7 A;  3PIO S;  1ZJW A;  1QRU A;  3PIP S;  1GTR A;  1DFU P;  1B75 A;  1QRS A;  5BNZ A;  4WF9 S;  5DM6 S;  2ZJQ S;  2ZJR S;  5GAG W;  1O0B A;  5GAH W;  4WFN S;  1D6K A;  2RD2 A;  4IOC S;  1O0C A;  5HL7 S;  1EUQ A;  4UY8 8;  2RE8 A;  4IOA S;  5JVH S;  4JXX A;  1QTQ A;  1NYL A;  4U67 S;  3DLL S;  4JYZ A;  4P2B A;  4WFA S;  1GTS A;  5JVG S;  4H3S A; 
#chains in the Genus database with same CATH topology
 2O5J A;  2Y0S D;  3AII A;  3HOZ C;  3KW2 A;  1TWC C;  1TWG C;  4OIP A;  4AYB D;  1QRT A;  4ZH4 A;  4LJZ A;  4A3C C;  1FEU A;  2NVY C;  2A68 A;  2BE5 A;  3GTM C;  1DFU P;  1GTR A;  1B75 A;  3S15 C;  1QRS A;  4V19 4;  2ZJR S;  1O0B A;  5GAH W;  3X1L B;  5C44 C;  4C3J C;  3GTK C;  3HKZ D;  4IOC S;  4OIR A;  3LYW A;  1Z85 A;  5HL7 S;  1R9T C;  3GTL C;  3CZB A;  5IYC C;  5IYD C;  4LLG A;  1QTQ A;  1YNJ A;  1NYL A;  3W2W B;  4J3C A;  4LK0 A;  2A6E A;  4JYZ A;  4G7H A;  2O5I A;  4P2B A;  4A3L C;  4Q5S A;  3HOX C;  3GTG C;  1V6Z A;  3EQL A;  4KN4 A;  2PNW A;  5JVG S;  3WOD A;  4G7Z A;  4OIQ A;  1QRU A;  4H3S A;  2B63 C;  3GTO C;  1SMY A;  1EUY A;  2KPU A;  2KQ1 A;  3I4N C;  5TMC A;  2ZJP S;  4YG2 A;  4MEY A;  2VUM C;  5GAD W;  3J7Z V;  4BBS C;  2L3U A;  4XLP A;  3S1R C;  4E8B A;  3GTQ C;  2E2I C;  3CQZ C;  4XSZ A;  2E2J C;  4H4K A;  4G7O A;  2HZ7 A;  4BY1 C;  2AE0 X;  5C4X C;  4Y52 C;  4Q4Z A;  2JA6 C;  2YU9 C;  4WF9 S;  1VHK A;  4A3D C;  2ZJQ S;  3PO3 C;  4GZY A;  4KMU A;  2CW0 A;  1SFO C;  2NVX C;  2RD2 A;  3S1Q C;  2RE8 A;  4OIN A;  2A6H A;  2PJJ A;  4Y7N C;  2KXY A;  3H3V D;  4C3H C;  2PIC A;  4U67 S;  1TWF C;  4C3I C;  4NOI A;  1I3Q C;  1HQM A;  2PPB A;  3GTP C;  1GTS A;  1WCM C;  5IZN A;  4WFB S;  3H0G C;  4A3E C;  1NXZ A;  3S2H C;  4IO9 S;  4A3J C;  4X6A C;  4XLN A;  2JA7 C;  4QJV A;  4YFX A;  4JXZ A;  2NWA A;  4BBR C;  1Y1W C;  3S2D C;  3FKI C;  4OIO A;  4MEX A;  4YFK A;  1UDX A;  5DM6 S;  4MQ9 A;  5GAG W;  2NVQ C;  4WFN S;  3S16 C;  5HQH A;  4BXX C;  1I50 C;  1EUQ A;  4UY8 8;  3GTJ C;  4IOA S;  1K83 C;  2PMZ D;  3HOY C;  4JK1 A;  5IP9 C;  3RZD C;  3HOU C;  4XSX A;  1TWH C;  3DLL S;  1VHY A;  4WFA S;  3S17 C;  4A3F C;  2EGW A;  1I6H C;  1YNN A;  5IYB C;  5C4J C;  3HOV C;  3M3Y C;  5C3E C;  1BDF A;  4A3G C;  2R7Z C;  4A93 C;  2EGV A;  4WCE S;  2G6G A;  2GAE A;  4KN7 A;  3M4O C;  2R93 C;  5TMF A;  1EXD A;  2NVT C;  4L69 A;  2PI8 A;  3CF5 S;  2R92 C;  3DXJ A;  3K7A C;  5DM7 S;  2PA8 D;  4A3M C;  5GAE W;  3S1N C;  3I4M C;  3S1M C;  1ZJW A;  3PIO S;  3PIP S;  5D4D A;  2G5D A;  5BNZ A;  3PO2 C;  2L5N A;  3S14 C;  1D6K A;  2WAQ D;  1O0C A;  5IP7 C;  2A69 A;  2JA5 C;  2WB1 D;  2Z0Y A;  4A3I C;  5JVH S;  4JXX A;  5FLM C;  2E2H C;  1IW7 A;  2JA8 C;  4A3K C;  3RZO C;  2CX8 A;  3HOW C;  4BY7 C;  4C2M C;  4A3B C;  1Y1V C;  1I6V A;  3W2V B;  4LK1 A;  4YFN A;  1ZYR A;  1TWA C;  4QIW D; 
#chains in the Genus database with same CATH homology
 5IZN A;  4WFB S;  1EUY A;  3AII A;  4IO9 S;  4WCE S;  2ZJP S;  5GAD W;  3J7Z V;  1EXD A;  3CF5 S;  1QRT A;  5DM7 S;  5GAE W;  4JXZ A;  1FEU A;  4H4K A;  2HZ7 A;  3PIO S;  1ZJW A;  1QRU A;  3PIP S;  1GTR A;  1DFU P;  1B75 A;  1QRS A;  5BNZ A;  4WF9 S;  4V19 4;  5DM6 S;  1UDX A;  2ZJQ S;  5GAG W;  2ZJR S;  5GAH W;  1O0B A;  3X1L B;  4WFN S;  1D6K A;  2RD2 A;  4IOC S;  1O0C A;  5HL7 S;  1EUQ A;  4UY8 8;  2RE8 A;  4IOA S;  5JVH S;  4JXX A;  1QTQ A;  1NYL A;  3W2W B;  4U67 S;  3DLL S;  4JYZ A;  4P2B A;  4WFA S;  3W2V B;  1GTS A;  5JVG S;  4H3S 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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#similar chains in the pdb database (?% sequence similarity)
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