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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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
molecule keywords 23S ribosomal RNA
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
2RD2A 4IOAS 5IZNA 4P2BA 4WFBS 2ZJPS 4UY88 3AIIA 4H3SA 1EUYA 2ZJRS 3PIPS 1GTRA 1QRUA 4WFNS 4JXZA 4WF9S 4U67S 1ZJWA 5HL7S 5DM7S 4IO9S 2ZJQS 3DLLS 1QRTA 5BNZA 3J7ZV 5GAEW 1QTQA 2RE8A 4WFAS 5GADW 1D6KA 1GTSA 4IOCS 1B75A 3PIOS 5DM6S 2HZ7A 4JXXA 4WCES 1EXDA 1EUQA 1O0BA 1FEUA 5JVGS 1DFUP 3CF5S 1QRSA 5GAHW 1NYLA 4JYZA 5GAGW 1O0CA 5JVHS
chains in the Genus database with same CATH superfamily
1UDXA 1Y1WC 1BDFA 3AIIA 3CZBA 4A3JC 3GTGC 5C44C 4V194 1EUYA 3DXJA 2PMZD 2NVTC 4KMUA 4OINA 2WB1D 3GTLC 3M4OC 4OIPA 3I4MC 3H3VD 3HOWC 4BBRC 3S15C 2BE5A 3DLLS 1QRTA 1I6HC 1VHYA 2PA8D 4ZH4A 4WFAS 3GTJC 3GTPC 1R9TC 4G7OA 4A3IC 3I4NC 4GZYA 3PIOS 5DM6S 2HZ7A 2Z0YA 1ZYRA 4KN4A 5FLMC 3S1NC 4C2MC 2JA5C 4BXXC 4JYZA 5GAGW 1TWFC 4JK1A 4A3CC 4IOAS 5IZNA 4H4KA 4LLGA 3LYWA 2ZJPS 3RZOC 4BY1C 5TMCA 2EGWA 4A3GC 3S16C 3GTMC 5D4DA 3S2HC 4Y7NC 1GTRA 1TWCC 4XLPA 1QRUA 4WFNS 4JXZA 1I3QC 4LJZA 4QIWD 4U67S 4Q5SA 5DM7S 4YFXA 2O5IA 4IO9S 3S1QC 2R7ZC 5BNZA 3J7ZV 4MQ9A 4OIRA 4YFNA 1TWAC 2GAEA 4LK0A 2PICA 5IP9C 1D6KA 4MEYA 4IOCS 1IW7A 3S1RC 4OIQA 2PJJA 4AYBD 2R92C 2E2JC 1EUQA 4A3FC 1O0BA 4QJVA 1Z85A 5IYDC 3EQLA 3CF5S 3CQZC 4XSZA 4E8BA 5IP7C 5TMFA 2JA6C 4J3CA 2RD2A 3GTKC 4WFBS 4G7HA 1YNJA 1TWGC 1NXZA 4UY88 2R93C 4C3IC 4H3SA 2PPBA 5C4JC 2JA7C 4A93C 2ZJRS 3KW2A 4L69A 4NOIA 3HOVC 3K7AC 4LK1A 5IYBC 3GTOC 2Y0SD 1V6ZA 2ZJQS 4OIOA 4X6AC 2CX8A 3M3YC 2KQ1A 1QTQA 2RE8A 1SMYA 3HKZD 5GADW 4Y52C 1WCMC 1GTSA 1B75A 3WODA 2KXYA 4YFKA 4WCES 1EXDA 2G5DA 4KN7A 1FEUA 4XSXA 5JVGS 3HOXC 4A3DC 5C4XC 3W2VB 3GTQC 4A3LC 2E2HC 3S1MC 2E2IC 3H0GC 4MEXA 2A68A 3HOUC 4C3JC 2YU9C 2L3UA 4A3KC 4BBSC 1Y1VC 4P2BA 1VHKA 5HQHA 5IYCC 1TWHC 2B63C 1SFOC 4YG2A 2A6EA 2G6GA 3PIPS 2KPUA 2L5NA 4Q4ZA 4G7ZA 2A6HA 4WF9S 2EGVA 2NVYC 1HQMA 1ZJWA 2WAQD 3PO3C 5HL7S 2CW0A 3HOZC 2NVXC 2AE0X 3HOYC 2NVQC 5GAEW 4BY7C 2PNWA 3S2DC 3PO2C 4C3HC 2JA8C 2NWAA 2VUMC 1I6VA 2O5JA 3RZDC 4JXXA 4XLNA 1YNNA 3W2WB 1I50C 1DFUP 2A69A 4A3BC 2PI8A 1QRSA 1K83C 3X1LB 5GAHW 1NYLA 5C3EC 4A3EC 3S14C 1O0CA 3FKIC 3S17C 5JVHS 4A3MC
chains in the Genus database with same CATH topology
1UDXA 2RD2A 5IZNA 4H4KA 4P2BA 4WFBS 4IOAS 2ZJPS 4UY88 3AIIA 4H3SA 4V194 1EUYA 2ZJRS 3PIPS 1GTRA 1QRUA 4WFNS 4JXZA 4WF9S 4U67S 1ZJWA 5HL7S 5DM7S 4IO9S 2ZJQS 3DLLS 1QRTA 5BNZA 3J7ZV 5GAEW 1QTQA 2RE8A 4WFAS 5GADW 1D6KA 1GTSA 4IOCS 1B75A 3PIOS 5DM6S 2HZ7A 4JXXA 4WCES 1EXDA 1EUQA 1O0BA 1FEUA 5JVGS 3W2VB 3W2WB 1DFUP 3CF5S 1QRSA 3X1LB 5GAHW 1NYLA 4JYZA 5GAGW 1O0CA 5JVHS
chains in the Genus database with same CATH homology


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