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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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
molecule keywords 23S ribosomal RNA
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
1GTSA 5IZNA 4H3SA 4WF9S 3DLLS 3CF5S 1FEUA 1ZJWA 1EUQA 3PIPS 5JVHS 1B75A 2ZJRS 5GAHW 2ZJPS 5BNZA 1EUYA 1GTRA 4WFAS 4JXXA 1NYLA 1QRSA 4P2BA 2RD2A 5JVGS 4IOCS 4JXZA 5HL7S 4IO9S 1EXDA 3PIOS 5GAGW 1O0CA 4WFBS 4IOAS 5GADW 4WCES 1O0BA 5DM7S 1QRUA 3AIIA 5DM6S 3J7ZV 4U67S 4UY88 1DFUP 4WFNS 2RE8A 1QTQA 4JYZA 1D6KA 5GAEW 2ZJQS 2HZ7A 1QRTA
chains in the Genus database with same CATH superfamily
1GTSA 2R92C 2PJJA 5IZNA 3HOVC 4BY7C 1TWCC 3RZDC 4H3SA 1WCMC 2O5IA 1HQMA 1FEUA 4A93C 3W2WB 1ZJWA 2JA6C 2NWAA 1B75A 4YFKA 1I3QC 2E2HC 3PO3C 5BNZA 5HQHA 2PNWA 4KN4A 1QRSA 2A6HA 4XSZA 2A69A 4MQ9A 3S15C 3M3YC 2JA7C 1TWAC 4A3EC 3GTQC 1YNNA 5D4DA 4IOAS 1K83C 2HZ7A 4YFXA 2L3UA 4AYBD 2KXYA 4WFNS 3DXJA 5FLMC 3GTOC 3GTGC 3CQZC 4ZH4A 4LK0A 5IYBC 3S1MC 3HOXC 1I50C 2KPUA 3M4OC 2O5JA 4J3CA 3DLLS 3RZOC 3X1LB 4NOIA 4OIOA 2NVQC 5IYDC 5TMFA 4MEXA 4QIWD 1VHKA 3PIPS 5JVHS 2ZJRS 3KW2A 4XLNA 4YFNA 2ZJPS 5C44C 1GTRA 3FKIC 1UDXA 2PA8D 4C2MC 3H3VD 1I6VA 4KMUA 4OINA 3I4NC 4XSXA 4A3CC 4A3IC 5C4XC 4A3GC 4Q5SA 5JVGS 5HL7S 4IO9S 4A3BC 4V194 5C4JC 3S16C 4LJZA 2NVTC 2EGVA 4JK1A 5GADW 1O0BA 1QRUA 3K7AC 2JA8C 3AIIA 4G7OA 4E8BA 4U67S 3J7ZV 4BBRC 1IW7A 1QTQA 3W2VB 4JYZA 1R9TC 2NVXC 1D6KA 1NXZA 2A6EA 4A3JC 3S17C 2PPBA 3WODA 2G6GA 1QRTA 2CX8A 3PO2C 3S2DC 4WF9S 4H4KA 2A68A 3EQLA 1SFOC 1YNJA 4A3MC 2JA5C 2PI8A 5IP7C 2NVYC 2PMZD 1EUYA 4XLPA 2R7ZC 4X6AC 1TWFC 2PICA 1NYLA 4A3FC 3LYWA 1Z85A 4Y7NC 4P2BA 2RD2A 4IOCS 4JXZA 1ZYRA 3GTPC 1V6ZA 4C3IC 4G7HA 1EXDA 3HKZD 1O0CA 2CW0A 4A3LC 3GTMC 4Q4ZA 4YG2A 4WCES 5DM7S 4LK1A 5DM6S 4UY88 1DFUP 1BDFA 3I4MC 3S1NC 1TWHC 4BXXC 4C3HC 2RE8A 2L5NA 2YU9C 5GAEW 4OIRA 5IYCC 1VHYA 4KN7A 2Z0YA 3S1RC 4A3DC 4QJVA 3H0GC 1SMYA 1Y1VC 1EUQA 4LLGA 4C3JC 3S1QC 2WB1D 3GTLC 5C3EC 3HOYC 5GAHW 2WAQD 2KQ1A 3S2HC 4BBSC 3GTJC 1Y1WC 4GZYA 5IP9C 3HOZC 2E2JC 5TMCA 4WFAS 2EGWA 4BY1C 4JXXA 3HOUC 1TWGC 3GTKC 3CZBA 2GAEA 2R93C 2E2IC 2BE5A 3HOWC 4A3KC 4OIQA 3S14C 5GAGW 3PIOS 4WFBS 2B63C 2VUMC 4MEYA 4G7ZA 2G5DA 1I6HC 4Y52C 2ZJQS 3CF5S 2Y0SD 4L69A 2AE0X 4OIPA
chains in the Genus database with same CATH topology
1GTSA 5IZNA 4H3SA 4WF9S 4H4KA 3DLLS 3CF5S 3X1LB 1FEUA 3W2WB 1ZJWA 1EUQA 3PIPS 5JVHS 1B75A 2ZJRS 5GAHW 2ZJPS 5BNZA 1EUYA 1GTRA 1UDXA 4WFAS 4JXXA 1NYLA 1QRSA 4P2BA 2RD2A 5JVGS 4IOCS 4JXZA 5HL7S 4IO9S 4V194 1EXDA 5GAGW 3PIOS 1O0CA 4WFBS 4IOAS 5GADW 4WCES 1O0BA 5DM7S 1QRUA 3AIIA 5DM6S 3J7ZV 4U67S 4UY88 1DFUP 4WFNS 2RE8A 1QTQA 3W2VB 4JYZA 1D6KA 5GAEW 2ZJQS 2HZ7A 1QRTA
chains in the Genus database with same CATH homology


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