3DLLS

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect trna positioning
Total Genus 21
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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
21
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
publication title The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
pubmed doi rcsb
molecule keywords rRNA-23S ribosomal RNA
total genus 21
structure length 175
sequence length 175
ec nomenclature
pdb deposition date 2008-06-27

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 3dllS01
2.170.120.20 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 Ribosomal protein L25, beta domain 3dllS02
2ZJPS 1QTQA 1O0BA 3J7ZV 2ZJRS 1QRUA 3AIIA 2RE8A 5GAHW 1GTRA 3PIPS 4IOCS 4WF9S 1B75A 4IOAS 5HL7S 5IZNA 2ZJQS 1DFUP 4JXXA 5GADW 1D6KA 5GAGW 1ZJWA 3DLLS 5BNZA 4IO9S 5JVGS 4WFNS 4P2BA 1EUYA 4UY88 5DM7S 1GTSA 1EXDA 5JVHS 1QRTA 5GAEW 1EUQA 1FEUA 1NYLA 4WFBS 1O0CA 3CF5S 4WCES 5DM6S 2RD2A 4JXZA 4U67S 1QRSA 3PIOS 4H3SA 4JYZA 4WFAS 2HZ7A
chains in the Genus database with same CATH superfamily
2ZJPS 2NVYC 3J7ZV 2ZJRS 3W2VB 3AIIA 1K83C 4C3JC 3GTGC 5C3EC 4BY7C 3DXJA 3CZBA 1NXZA 3PO3C 2KXYA 2G6GA 4IO9S 5JVGS 4UY88 1EUYA 1VHKA 1YNNA 5DM7S 1GTSA 4LJZA 4MEYA 2L5NA 2YU9C 2EGWA 1Y1VC 3GTMC 3W2WB 4MQ9A 1TWFC 1R9TC 1FEUA 2NVXC 3GTLC 5C4XC 2R7ZC 3CF5S 2WB1D 2GAEA 4JK1A 4QIWD 4YG2A 4C3IC 4YFXA 3S1RC 2CW0A 4U67S 5C4JC 3HOZC 4XLPA 3I4MC 4QJVA 3PIOS 4H3SA 2PMZD 2R92C 3S14C 3M4OC 1YNJA 3S15C 2R93C 4WFAS 2A69A 2AE0X 3S1NC 4H4KA 2PI8A 3GTOC 4G7OA 4AYBD 4YFNA 4Q5SA 1UDXA 2BE5A 2O5JA 5HL7S 4A3MC 4V194 4MEXA 5GADW 2EGVA 2A6EA 4Q4ZA 3HOXC 4G7ZA 3RZDC 5IYDC 4G7HA 3DLLS 2L3UA 2E2HC 4P2BA 5IYBC 3GTJC 4Y7NC 3HOWC 2JA5C 1I50C 5FLMC 2O5IA 2JA7C 5GAEW 3S1QC 2CX8A 4LK1A 4A3KC 4A3BC 1I6HC 1O0CA 4C2MC 2E2JC 1SMYA 5IP9C 4WCES 1ZYRA 2PPBA 3H3VD 2PA8D 5DM6S 4JXZA 4XSXA 1QRSA 3RZOC 3KW2A 3HOVC 5IP7C 4JYZA 2B63C 3I4NC 2KPUA 4L69A 3S2HC 1O0BA 2PJJA 4A3IC 3LYWA 5C44C 5TMFA 4C3HC 4OIQA 1TWAC 2RE8A 2JA6C 3HOYC 3M3YC 1B75A 1Y1WC 4A3JC 1V6ZA 2ZJQS 1DFUP 4GZYA 4JXXA 4NOIA 4YFKA 5D4DA 3GTPC 2VUMC 2Z0YA 2PNWA 4A93C 3HOUC 4LK0A 3WODA 2KQ1A 3GTKC 3PO2C 3S17C 1HQMA 4XLNA 2NWAA 1Z85A 1NYLA 4WFBS 4ZH4A 3S16C 1I3QC 3FKIC 2RD2A 2JA8C 1IW7A 3EQLA 2E2IC 1WCMC 2A68A 4A3CC 4WF9S 2HZ7A 1QTQA 1QRUA 4LLGA 3GTQC 4BBRC 4OINA 5GAHW 1GTRA 3HKZD 3PIPS 4IOCS 4BY1C 5IYCC 3CQZC 4IOAS 5TMCA 4A3LC 2WAQD 5IZNA 5HQHA 3S1MC 1D6KA 3K7AC 5GAGW 1ZJWA 4A3GC 4OIOA 4OIRA 2Y0SD 4OIPA 4E8BA 4Y52C 5BNZA 2G5DA 4WFNS 3X1LB 4A3FC 4BXXC 2NVQC 1EXDA 4X6AC 5JVHS 4KN7A 1TWGC 3S2DC 4A3DC 2PICA 1EUQA 2NVTC 3H0GC 1SFOC 1I6VA 4A3EC 1VHYA 1TWHC 1BDFA 1TWCC 4XSZA 4BBSC 4KN4A 4J3CA 4KMUA 1QRTA 2A6HA
chains in the Genus database with same CATH topology
2ZJPS 1QTQA 1O0BA 3J7ZV 2ZJRS 4H4KA 1QRUA 3W2VB 3AIIA 2RE8A 5GAHW 1GTRA 3PIPS 4IOCS 4WF9S 1UDXA 1B75A 4IOAS 5HL7S 5IZNA 4V194 2ZJQS 1DFUP 4JXXA 5GADW 1D6KA 5GAGW 1ZJWA 3DLLS 5BNZA 4IO9S 5JVGS 4WFNS 4P2BA 1EUYA 4UY88 5DM7S 1GTSA 3X1LB 1EXDA 5JVHS 1QRTA 5GAEW 3W2WB 1EUQA 1FEUA 1NYLA 4WFBS 1O0CA 3CF5S 4WCES 5DM6S 2RD2A 4JXZA 4U67S 1QRSA 3PIOS 4H3SA 4JYZA 4WFAS 2HZ7A
chains in the Genus database with same CATH homology


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