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


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