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
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 rRNA-23S ribosomal RNA
publication title The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
pubmed doi rcsb
molecule tags Ribosome
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
4H3SA 3AIIA 5DM6S 4WFBS 3PIPS 4JXXA 2HZ7A 1O0CA 3PIOS 3CF5S 4WFNS 4WCES 5JVHS 1GTRA 5GADW 4UY88 4P2BA 1QTQA 5BNZA 4JYZA 3DLLS 5IZNA 4JXZA 1ZJWA 1EXDA 4IOAS 1QRTA 4WFAS 4WF9S 2ZJRS 2RE8A 5JVGS 1QRSA 5HL7S 4IO9S 1DFUP 1B75A 5GAHW 5GAEW 1EUYA 1NYLA 5DM7S 5GAGW 1D6KA 1GTSA 3J7ZV 4U67S 2ZJQS 2ZJPS 1O0BA 1QRUA 1FEUA 1EUQA 4IOCS 2RD2A
chains in the Genus database with same CATH superfamily
4H3SA 5IP7C 3AIIA 5DM6S 5C44C 4JXXA 1R9TC 2E2HC 4OIOA 3HOXC 3PIOS 2BE5A 3CF5S 2E2JC 3HOZC 3S14C 4BY7C 4A3GC 1I50C 4G7OA 3K7AC 4P2BA 4A93C 5HQHA 3CZBA 2L5NA 2PICA 3FKIC 4A3JC 4OIQA 2KPUA 2EGWA 4C2MC 3H3VD 3DLLS 4A3FC 5IZNA 3CQZC 4XSZA 3M3YC 2AE0X 4H4KA 4C3JC 3HOYC 4WFAS 3HOUC 3KW2A 2ZJRS 5FLMC 5C3EC 3S1MC 3WODA 1QRSA 2KQ1A 5D4DA 1DFUP 4LK0A 5IP9C 5IYDC 4A3DC 1YNNA 2O5JA 2VUMC 4QJVA 2Z0YA 2PPBA 2RD2A 3PO2C 2L3UA 2PI8A 4LLGA 1Y1VC 3HKZD 1VHYA 4Q4ZA 3EQLA 4WCES 4LJZA 4Y52C 2A68A 2G6GA 4G7HA 2E2IC 2B63C 2JA5C 1ZYRA 2PJJA 3HOVC 1QTQA 3I4MC 1SFOC 4Y7NC 4IOAS 2WAQD 3H0GC 2CX8A 2GAEA 2R92C 4WF9S 3W2WB 4MEXA 3GTJC 2NVTC 4E8BA 4A3IC 1V6ZA 4A3EC 2R7ZC 1NYLA 5DM7S 5GAGW 1GTSA 3S1RC 3S15C 3J7ZV 3S2HC 3S2DC 2ZJPS 1I6VA 1HQMA 2Y0SD 1EUQA 1UDXA 1TWCC 4IOCS 4YG2A 3RZDC 4OIPA 4A3BC 1TWGC 4C3HC 4WFBS 3PIPS 1I3QC 4BY1C 4A3CC 3LYWA 1IW7A 1O0CA 1I6HC 4YFKA 5JVHS 2JA8C 1Z85A 4UY88 2G5DA 3GTLC 3GTKC 4BBRC 5BNZA 3GTGC 5TMFA 3RZOC 1YNJA 4G7ZA 4YFXA 1ZJWA 1EXDA 3S16C 1NXZA 2PA8D 4KN7A 4NOIA 2A6HA 4A3MC 4JK1A 3PO3C 3S1NC 3DXJA 4MQ9A 1SMYA 2RE8A 1TWFC 4J3CA 4LK1A 5IYCC 3S1QC 4IO9S 1B75A 1BDFA 5GAHW 2WB1D 5GAEW 5IYBC 2YU9C 1D6KA 1TWHC 2PNWA 4U67S 1FEUA 3GTQC 1O0BA 4X6AC 2PMZD 4XSXA 2HZ7A 4WFNS 4BXXC 4OIRA 3GTPC 5C4XC 1GTRA 2R93C 4KMUA 5GADW 4A3KC 3GTOC 5TMCA 3GTMC 1VHKA 2NVYC 2JA6C 4JYZA 4AYBD 2EGVA 2NWAA 4XLNA 3I4NC 2NVQC 4KN4A 1Y1WC 3X1LB 2JA7C 4JXZA 2CW0A 4V194 5C4JC 2NVXC 1TWAC 1QRTA 4YFNA 4GZYA 4XLPA 4Q5SA 4ZH4A 3W2VB 5JVGS 2KXYA 3S17C 2O5IA 5HL7S 4A3LC 2A69A 4L69A 1EUYA 3HOWC 4MEYA 4QIWD 2A6EA 2ZJQS 3M4OC 1QRUA 1WCMC 4C3IC 4OINA 4BBSC 1K83C
chains in the Genus database with same CATH topology
4H3SA 3AIIA 5DM6S 4WFBS 3PIPS 4JXXA 2HZ7A 1O0CA 3PIOS 3CF5S 4WFNS 4WCES 5JVHS 1GTRA 5GADW 4UY88 4P2BA 1QTQA 5BNZA 4JYZA 3DLLS 5IZNA 3X1LB 4JXZA 4H4KA 1ZJWA 1EXDA 4V194 4IOAS 1QRTA 4WFAS 1EUQA 4WF9S 2ZJRS 3W2WB 3W2VB 2RE8A 5JVGS 1QRSA 5HL7S 4IO9S 1DFUP 1B75A 5GAHW 5GAEW 1EUYA 1NYLA 5DM7S 5GAGW 1D6KA 1GTSA 3J7ZV 4U67S 2ZJQS 2ZJPS 1O0BA 1QRUA 1FEUA 1UDXA 4IOCS 2RD2A
chains in the Genus database with same CATH homology


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