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


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