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


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