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


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