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


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