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


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