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


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