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


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