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


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