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


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