3PIOS

Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit
Total Genus 14
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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
14
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/antibiotic
molecule keywords RIBOSOMAL 23S RNA
publication title Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.
pubmed doi rcsb
total genus 14
structure length 175
sequence length 175
ec nomenclature
pdb deposition date 2010-11-07

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 3pioS01
2.170.120.20 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 Ribosomal protein L25, beta domain 3pioS02
1QRTA 4WFAS 1GTSA 5GAGW 5GAHW 1QRUA 1O0BA 4H3SA 3AIIA 2ZJQS 4IOCS 1GTRA 1QRSA 1B75A 2RD2A 5BNZA 1EUQA 5JVGS 4IOAS 4U67S 1O0CA 4WCES 3PIOS 3PIPS 1ZJWA 3DLLS 4WFNS 5HL7S 2ZJPS 5JVHS 5DM6S 1EXDA 5DM7S 3CF5S 5GADW 5GAEW 4JYZA 4WF9S 4JXZA 1QTQA 4P2BA 1DFUP 1D6KA 1NYLA 4WFBS 2HZ7A 1EUYA 4JXXA 5IZNA 2ZJRS 4UY88 2RE8A 1FEUA 3J7ZV 4IO9S
chains in the Genus database with same CATH superfamily
1WCMC 5D4DA 1UDXA 5IP9C 3HOYC 5GAGW 2R93C 4IOCS 1GTRA 3CZBA 1QRSA 4YFNA 2R92C 4A3DC 5BNZA 4BBSC 4IOAS 3S16C 4L69A 3S17C 3S14C 2PJJA 2JA6C 3I4MC 4YG2A 4E8BA 4OIQA 3HOWC 4A3MC 5JVHS 2WB1D 3M4OC 2PICA 3W2VB 5DM6S 4V194 1R9TC 5C3EC 2G5DA 3HOZC 2Z0YA 4C3IC 1IW7A 4G7ZA 4JYZA 3RZOC 4XLNA 4QIWD 4OIPA 2PMZD 1QTQA 1SMYA 2L5NA 3S1RC 3S1MC 4A3GC 2KQ1A 4JXXA 4NOIA 5IZNA 2JA7C 1Y1VC 2RE8A 1I3QC 4J3CA 3J7ZV 3S15C 1TWGC 2O5IA 4GZYA 4WFAS 4KMUA 2WAQD 1GTSA 4A3IC 2NVQC 2NWAA 5IYBC 2PPBA 3HOVC 3AIIA 4H3SA 3RZDC 2O5JA 1B75A 1TWCC 4Q5SA 3DXJA 2CX8A 1BDFA 3LYWA 4G7HA 1O0CA 4JK1A 4WCES 4A3JC 2G6GA 2JA5C 1ZJWA 3DLLS 5HL7S 1EXDA 5DM7S 2BE5A 5HQHA 1VHYA 4A93C 2JA8C 4G7OA 5GAEW 4Y7NC 1Y1WC 3GTGC 2EGVA 2R7ZC 4XSZA 4P2BA 1YNJA 3K7AC 2YU9C 1D6KA 1NYLA 1EUYA 2HZ7A 3S1NC 5IYCC 4YFXA 5FLMC 4BY7C 4BY1C 2A6HA 2NVTC 3GTPC 1FEUA 3GTOC 4LK1A 3GTMC 4C3HC 3HOUC 2E2HC 2GAEA 4LLGA 5IYDC 1I50C 3HOXC 2Y0SD 3I4NC 1SFOC 3S1QC 2A69A 2RD2A 2EGWA 3H3VD 1NXZA 2CW0A 4A3KC 2PI8A 3W2WB 3X1LB 4LJZA 2A68A 4ZH4A 4KN4A 4C3JC 3CQZC 5TMCA 3M3YC 4MQ9A 1I6HC 4A3BC 1YNNA 4BBRC 3FKIC 2L3UA 2PA8D 2E2IC 3PO3C 4Q4ZA 4JXZA 4LK0A 2PNWA 2KPUA 2E2JC 2A6EA 3GTJC 3PO2C 4WFBS 4KN7A 4XSXA 4MEXA 4A3EC 3EQLA 3H0GC 3GTQC 4IO9S 1QRTA 4YFKA 4MEYA 1TWAC 1TWFC 4Y52C 2VUMC 1ZYRA 3KW2A 5GAHW 1QRUA 4QJVA 5C4JC 3GTLC 1O0BA 2ZJQS 5TMFA 4A3CC 2KXYA 1EUQA 4OIOA 5C44C 4OIRA 5JVGS 3HKZD 3S2DC 4U67S 2AE0X 4A3FC 4H4KA 3PIOS 1K83C 2NVYC 3PIPS 3S2HC 1Z85A 4WFNS 2ZJPS 1V6ZA 1HQMA 5IP7C 3CF5S 2NVXC 3GTKC 1VHKA 5GADW 2B63C 4WF9S 3WODA 5C4XC 1DFUP 4AYBD 1I6VA 4X6AC 2ZJRS 4UY88 4C2MC 4XLPA 4OINA 1TWHC 4A3LC 4BXXC
chains in the Genus database with same CATH topology
1QRTA 4WFAS 1UDXA 1GTSA 5GAGW 5GAHW 1QRUA 1O0BA 3AIIA 4H3SA 2ZJQS 4IOCS 1GTRA 1QRSA 1B75A 2RD2A 5BNZA 1EUQA 5JVGS 4IOAS 4U67S 3W2WB 1O0CA 3X1LB 4H4KA 4WCES 3PIOS 3PIPS 1ZJWA 3DLLS 4WFNS 5HL7S 3W2VB 2ZJPS 5DM6S 5JVHS 1EXDA 5DM7S 4V194 3CF5S 5GADW 5GAEW 4JYZA 4WF9S 4JXZA 1QTQA 4P2BA 1DFUP 1D6KA 1NYLA 4WFBS 2HZ7A 1EUYA 4JXXA 5IZNA 2ZJRS 4UY88 2RE8A 1FEUA 3J7ZV 4IO9S
chains in the Genus database with same CATH homology


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