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


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