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


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