3PIPS

Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit
Total Genus 15
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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
15
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 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 15
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 3pipS01
2.170.120.20 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 Ribosomal protein L25, beta domain 3pipS02
4WCES 5IZNA 4JYZA 4JXXA 4IO9S 1EXDA 4WFAS 3PIOS 1EUQA 1GTRA 5GAHW 5DM6S 2ZJPS 4UY88 4JXZA 5BNZA 1DFUP 1B75A 1O0CA 1EUYA 4H3SA 4WFBS 2ZJRS 5GAEW 3J7ZV 5JVGS 2ZJQS 4U67S 4P2BA 3CF5S 5GADW 2HZ7A 1QRSA 3AIIA 3DLLS 4IOAS 1O0BA 3PIPS 4WF9S 1ZJWA 5JVHS 1QRUA 2RD2A 4IOCS 1QRTA 2RE8A 1NYLA 1D6KA 4WFNS 1GTSA 1FEUA 5HL7S 1QTQA 5DM7S 5GAGW
chains in the Genus database with same CATH superfamily
2EGVA 4WCES 5IZNA 3EQLA 4JYZA 3RZOC 4QIWD 4ZH4A 2YU9C 1TWAC 4WFAS 4A3GC 3PIOS 4LK1A 2R7ZC 4A3DC 1TWCC 2G5DA 2PPBA 3X1LB 1DFUP 4OIQA 2CX8A 2A68A 1TWGC 4YFKA 2BE5A 3M3YC 4NOIA 5IYDC 5FLMC 4Y7NC 3S1QC 1QRSA 3HOZC 3AIIA 3DLLS 3GTOC 3W2VB 4BY1C 4C3IC 1ZYRA 1WCMC 1Y1WC 2NWAA 4A3BC 3I4NC 3DXJA 2A6HA 5C4JC 2EGWA 3H3VD 3HOWC 3I4MC 1TWHC 4JK1A 3WODA 2JA6C 1BDFA 2JA7C 4A3IC 3S1RC 4OINA 1VHKA 4GZYA 4G7ZA 5DM7S 1I6HC 5C3EC 2KQ1A 4JXXA 3S2DC 2Z0YA 1EXDA 1I6VA 1I3QC 4A3MC 1UDXA 2GAEA 5GAHW 3CQZC 2ZJPS 3K7AC 2PICA 4A3JC 1B75A 4A3FC 1EUYA 2NVXC 4H3SA 4WFBS 2ZJRS 2A69A 3RZDC 4A3LC 5GAEW 3J7ZV 4OIOA 4A3EC 2ZJQS 4U67S 3CF5S 4KN7A 5IYCC 2NVQC 2L5NA 2PJJA 2AE0X 2PMZD 2HZ7A 2L3UA 5D4DA 1YNJA 3PO3C 3KW2A 4YG2A 4C3HC 1V6ZA 1QRUA 2RE8A 2B63C 4J3CA 4WFNS 4G7OA 3S2HC 3GTKC 1GTSA 4V194 4LK0A 5TMCA 1QTQA 1SMYA 4OIRA 5C4XC 4G7HA 4H4KA 4IO9S 2A6EA 1K83C 4C2MC 3S1MC 2O5JA 1EUQA 4AYBD 4BBRC 3W2WB 3S16C 5DM6S 4L69A 4UY88 4QJVA 3HOYC 3S15C 2KXYA 4XLNA 4A3KC 4C3JC 3GTMC 5IP9C 4BBSC 1Z85A 3HOXC 5JVGS 4LJZA 4P2BA 2PA8D 2O5IA 2E2IC 1VHYA 2WAQD 1IW7A 3GTJC 2JA8C 3PO2C 4Q4ZA 3GTLC 3CZBA 1O0BA 2NVYC 3PIPS 4WF9S 1ZJWA 1HQMA 1Y1VC 5HQHA 1QRTA 1D6KA 4MQ9A 4E8BA 5IP7C 3GTQC 2PNWA 2NVTC 4LLGA 3HOVC 2PI8A 3GTPC 2R93C 1GTRA 1R9TC 4JXZA 2R92C 5BNZA 3HOUC 3H0GC 5TMFA 1O0CA 1I50C 4XSZA 4YFNA 2G6GA 3S1NC 1NXZA 4BXXC 4A3CC 4MEYA 2VUMC 2WB1D 2Y0SD 3S17C 4X6AC 4KMUA 4KN4A 4Y52C 5IYBC 3S14C 5GADW 2E2JC 4Q5SA 4YFXA 1YNNA 4IOAS 3HKZD 5C44C 4XSXA 4A93C 5JVHS 2JA5C 2RD2A 1TWFC 3M4OC 4IOCS 2CW0A 2E2HC 3GTGC 1NYLA 4OIPA 1SFOC 4XLPA 4MEXA 3LYWA 2KPUA 1FEUA 4BY7C 5HL7S 3FKIC 5GAGW
chains in the Genus database with same CATH topology
4WCES 5IZNA 4JYZA 4JXXA 4H4KA 4IO9S 1EXDA 4WFAS 3PIOS 1EUQA 1UDXA 1GTRA 5GAHW 3W2WB 5DM6S 2ZJPS 4UY88 3X1LB 5BNZA 4JXZA 1DFUP 1B75A 1O0CA 1EUYA 4H3SA 4WFBS 2ZJRS 5GAEW 3J7ZV 5JVGS 2ZJQS 4P2BA 4U67S 3CF5S 5GADW 2HZ7A 1QRSA 3AIIA 3DLLS 3W2VB 4IOAS 1O0BA 3PIPS 4WF9S 1ZJWA 5JVHS 1QRUA 2RD2A 4IOCS 1QRTA 2RE8A 1NYLA 1D6KA 4WFNS 1GTSA 4V194 1FEUA 5HL7S 1QTQA 5DM7S 5GAGW
chains in the Genus database with same CATH homology


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