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


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