5JVHS

The crystal structure large ribosomal subunit (50s) of deinococcus radiodurans in complex with evernimicin
Total Genus 19
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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
19
sequence length
179
structure length
179
Chain Sequence
b'MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPRLTAE'
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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 19
structure length 179
sequence length 179
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 5jvhS01
2.170.120.20 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 Ribosomal protein L25, beta domain 5jvhS02
4JYZA 1B75A 4H3SA 4WFBS 5BNZA 3PIOS 4P2BA 5JVHS 1O0CA 5DM6S 1EUYA 3CF5S 1FEUA 1QRSA 4JXXA 1QRUA 5GADW 5GAGW 4JXZA 1DFUP 4IOCS 1D6KA 1GTRA 4IOAS 1GTSA 4IO9S 1ZJWA 3PIPS 4UY88 1QTQA 5JVGS 2RD2A 4WFNS 5HL7S 3DLLS 2RE8A 1QRTA 3AIIA 2HZ7A 5GAEW 5IZNA 1EXDA 4WF9S 5DM7S 1NYLA 1EUQA 3J7ZV 4WCES 1O0BA 4U67S 2ZJPS 5GAHW 4WFAS 2ZJQS 2ZJRS
chains in the Genus database with same CATH superfamily
4QJVA 2O5IA 4XLPA 3HOVC 4JYZA 1B75A 2E2JC 3S1MC 5BNZA 4A3GC 5JVHS 3HOYC 4XSXA 2R92C 3CF5S 1FEUA 5C4XC 4JXZA 3PO2C 2KPUA 2PPBA 3HOUC 1I6HC 1GTRA 4Q5SA 4G7HA 1GTSA 3S2DC 2A68A 4ZH4A 3S17C 4UY88 2L5NA 5HQHA 2RD2A 1WCMC 3S2HC 1TWCC 5IYCC 4OIRA 3AIIA 3RZDC 2R93C 1UDXA 5IZNA 4WF9S 2A69A 2CW0A 4A3JC 3M3YC 1VHKA 4OINA 2ZJPS 1NXZA 4MEYA 4Y7NC 3H0GC 5IP7C 2A6EA 3H3VD 2PI8A 3S15C 4OIOA 1ZYRA 5TMFA 5TMCA 3I4NC 4H3SA 2NVTC 1TWAC 3S1NC 3DXJA 1BDFA 4AYBD 1QRSA 3S16C 4A3CC 3S1QC 5GAGW 5C4JC 4IOCS 1D6KA 3GTKC 1Y1VC 4YFXA 3GTQC 4YFNA 3DLLS 4XSZA 5D4DA 3GTPC 4C2MC 3GTJC 5FLMC 4WCES 4BY1C 3W2VB 2CX8A 1O0BA 3I4MC 2G5DA 2JA6C 4WFAS 2NVYC 4A3LC 2AE0X 1TWFC 3CQZC 1Y1WC 1YNJA 2ZJRS 1I50C 4E8BA 4C3IC 2PJJA 2NWAA 4Y52C 4A3BC 4P2BA 3FKIC 1SMYA 3WODA 5C3EC 2KQ1A 5DM6S 4LLGA 2L3UA 5IP9C 4H4KA 5GADW 3GTOC 1DFUP 3S1RC 3S14C 4IOAS 4BBSC 4V194 4C3JC 1ZJWA 4A3FC 1SFOC 4XLNA 1QTQA 4KMUA 5JVGS 2R7ZC 3CZBA 4A3MC 1V6ZA 2PNWA 4WFNS 2RE8A 2VUMC 4BXXC 4X6AC 1QRTA 3GTLC 2HZ7A 5GAEW 3HKZD 1EXDA 2WAQD 5DM7S 1NYLA 3X1LB 3K7AC 4NOIA 3J7ZV 1I3QC 4LJZA 4BY7C 2B63C 3W2WB 1TWGC 2PA8D 4MEXA 1VHYA 4GZYA 2KXYA 1R9TC 1HQMA 4MQ9A 4A93C 5C44C 3LYWA 2JA8C 4OIQA 2YU9C 4C3HC 4KN7A 4L69A 4WFBS 3GTGC 2O5JA 4A3DC 4YG2A 3PIOS 1O0CA 3HOXC 4Q4ZA 2GAEA 4QIWD 2EGWA 1K83C 2E2IC 2NVXC 1EUYA 3PO3C 1IW7A 2PMZD 4JXXA 3KW2A 1QRUA 2A6HA 4YFKA 4J3CA 2WB1D 1YNNA 4IO9S 3EQLA 3M4OC 3PIPS 4KN4A 2EGVA 4BBRC 5HL7S 2BE5A 4LK0A 4G7ZA 3RZOC 4OIPA 1EUQA 2Z0YA 3HOZC 4G7OA 4A3KC 4U67S 3HOWC 1I6VA 2PICA 5GAHW 1Z85A 1TWHC 2Y0SD 4JK1A 4A3EC 4A3IC 2E2HC 2JA7C 3GTMC 2JA5C 2NVQC 5IYBC 2ZJQS 2G6GA 4LK1A 5IYDC
chains in the Genus database with same CATH topology
4JYZA 1B75A 4H3SA 4WFBS 5BNZA 3PIOS 4P2BA 5JVHS 1O0CA 5DM6S 1EUYA 3CF5S 1FEUA 1QRSA 4JXXA 1QRUA 4H4KA 5GAGW 5GADW 4JXZA 1DFUP 4IOCS 1D6KA 1GTRA 4IOAS 1GTSA 4IO9S 4V194 1ZJWA 3PIPS 4UY88 1QTQA 5JVGS 2RD2A 4WFNS 5HL7S 3DLLS 2RE8A 1QRTA 3AIIA 2HZ7A 5GAEW 1UDXA 5IZNA 1EXDA 4WF9S 5DM7S 1NYLA 1EUQA 3X1LB 3J7ZV 4WCES 3W2VB 1O0BA 4U67S 2ZJPS 3W2WB 5GAHW 4WFAS 2ZJQS 2ZJRS
chains in the Genus database with same CATH homology


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