4IO9S

Crystal structure of compound 4d bound to large ribosomal subunit (50s) from deinococcus radiodurans
Total Genus 28
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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
28
sequence length
175
structure length
175
Chain Sequence
MELTAKPRTPKQKLDESMIAAVAYNKENNVSFALDRKAFDRAFRQQSTTGLFDITVEGGETFPALVKAVQMDKRKRAPIHVDFYMVTYGEPVEVSVPVHTTGRSQGEVQGGLVDIVVHNLQIVAPGPRRIPQELVVDVTKMNIGDHITAGDIKLPEGCTLAADPELTVVSVLPPR
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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 Novel 3-O-carbamoyl erythromycin A derivatives (carbamolides) with activity against resistant staphylococcal and streptococcal isolates.
pubmed doi rcsb
molecule tags Ribosome/ribosome inhibitor
total genus 28
structure length 175
sequence length 175
ec nomenclature
pdb deposition date 2013-01-07

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 4io9S01
2.170.120.20 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 Ribosomal protein L25, beta domain 4io9S02
2RE8A 4JXXA 3PIOS 4JYZA 4IO9S 1QRTA 1O0BA 3CF5S 2ZJRS 1EXDA 4H3SA 5DM7S 1EUQA 1QRSA 3J7ZV 5DM6S 1DFUP 4WCES 3AIIA 5HL7S 2RD2A 5GADW 3DLLS 2ZJPS 4P2BA 5GAGW 5JVHS 4IOCS 4WFBS 5BNZA 1B75A 1ZJWA 4UY88 5GAHW 4IOAS 5IZNA 4WFNS 5JVGS 2HZ7A 2ZJQS 1QTQA 1GTSA 1FEUA 4U67S 1EUYA 4WFAS 1NYLA 4JXZA 1QRUA 1GTRA 1D6KA 4WF9S 5GAEW 3PIPS 1O0CA
chains in the Genus database with same CATH superfamily
3M4OC 5TMFA 3PIOS 3EQLA 5IYBC 4H3SA 5DM7S 1TWAC 4A3FC 3KW2A 5C4XC 3I4NC 4KN7A 4LLGA 4OIPA 1TWFC 4G7HA 1R9TC 3RZOC 4BXXC 4A3CC 3S1QC 4ZH4A 2ZJPS 4IOCS 3RZDC 4AYBD 5C44C 4A3JC 4QIWD 2PMZD 4J3CA 4Y52C 3HOWC 2G5DA 1ZJWA 2A69A 2AE0X 5IZNA 1NXZA 2NVQC 4A3LC 2HZ7A 2ZJQS 3S1RC 3GTJC 1FEUA 2CW0A 3HOXC 4A3DC 2Y0SD 2PPBA 4WFAS 4OIRA 4A3GC 4C3HC 2WAQD 2VUMC 2GAEA 1ZYRA 3H3VD 3M3YC 1O0CA 3FKIC 3HOUC 3HOVC 2A6EA 2RE8A 3GTOC 2O5IA 3HOZC 3S2HC 4A3BC 1EXDA 1EUQA 1QRSA 3J7ZV 3GTLC 4YG2A 3HOYC 3W2WB 3CQZC 4LK1A 2PJJA 5FLMC 3S1NC 4BY7C 3DLLS 2E2HC 4YFKA 4P2BA 2KPUA 1VHYA 3H0GC 5IYCC 4MEXA 3I4MC 3PO2C 2O5JA 3W2VB 5BNZA 1IW7A 4GZYA 4OIOA 2NVXC 2EGVA 5IYDC 2A6HA 5GAHW 4Y7NC 3GTPC 1TWGC 3S14C 4XLPA 5JVGS 4BBSC 4KN4A 3GTGC 2PICA 1WCMC 4A3KC 1YNJA 4XLNA 1BDFA 2KXYA 4C2MC 3S1MC 4JXZA 1D6KA 4WF9S 3PIPS 2L5NA 3WODA 1UDXA 2YU9C 2L3UA 1QRTA 1V6ZA 1TWCC 1O0BA 2PI8A 3CZBA 2ZJRS 2PA8D 5TMCA 2NVTC 4LJZA 2R93C 3AIIA 4XSXA 4OINA 1HQMA 2NWAA 2KQ1A 1Y1WC 1YNNA 4BY1C 5C4JC 1I6VA 3HKZD 4YFXA 1TWHC 4A3MC 5D4DA 4LK0A 1I3QC 4OIQA 2NVYC 1VHKA 4WFNS 2BE5A 1K83C 2E2JC 4G7OA 4U67S 2CX8A 5C3EC 3PO3C 4XSZA 5HQHA 4C3JC 1GTRA 1I50C 5IP7C 3GTMC 2WB1D 2R92C 1SFOC 4YFNA 2JA6C 4JXXA 4IO9S 4JYZA 4MQ9A 1Y1VC 4A3IC 2G6GA 3CF5S 4BBRC 3LYWA 3GTQC 1I6HC 3X1LB 2JA8C 5DM6S 1DFUP 4V194 4WCES 5HL7S 2RD2A 4QJVA 3S2DC 4KMUA 4E8BA 1SMYA 2Z0YA 5GADW 5GAGW 4L69A 5JVHS 4WFBS 2JA7C 1Z85A 2EGWA 1B75A 4UY88 3DXJA 2PNWA 5IP9C 4IOAS 4Q5SA 1QTQA 1GTSA 3GTKC 2E2IC 4MEYA 4A93C 4C3IC 4X6AC 1EUYA 2R7ZC 2JA5C 4JK1A 1NYLA 2B63C 3S17C 4H4KA 1QRUA 3K7AC 4Q4ZA 4G7ZA 5GAEW 4NOIA 4A3EC 3S16C 3S15C 2A68A
chains in the Genus database with same CATH topology
2RE8A 4JXXA 3PIOS 4JYZA 4IO9S 1QRTA 1O0BA 3CF5S 2ZJRS 1EXDA 4H3SA 5DM7S 1EUQA 1QRSA 3X1LB 3J7ZV 5DM6S 1DFUP 4V194 3AIIA 4WCES 3W2WB 5HL7S 2RD2A 5GADW 3DLLS 2ZJPS 4P2BA 5GAGW 5JVHS 4IOCS 4WFBS 3W2VB 5BNZA 1B75A 1ZJWA 4UY88 5GAHW 4IOAS 5IZNA 4WFNS 5JVGS 2HZ7A 2ZJQS 1QTQA 1GTSA 1FEUA 4U67S 1EUYA 4WFAS 1NYLA 4H4KA 1QRUA 1GTRA 1D6KA 4JXZA 5GAEW 4WF9S 3PIPS 1O0CA 1UDXA
chains in the Genus database with same CATH homology


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