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


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