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


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