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


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