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


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