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


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