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


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