5DM6S

Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans
Total Genus 22
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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
22
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 50S ribosomal protein L1
molecule tags Ribosome
publication title Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
pubmed doi rcsb
total genus 22
structure length 175
sequence length 175
ec nomenclature
pdb deposition date 2015-09-08

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 5dm6S01
2.170.120.20 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 Ribosomal protein L25, beta domain 5dm6S02
1O0CA 2ZJPS 3DLLS 4IO9S 5HL7S 4WFBS 2ZJQS 5GAGW 1O0BA 5GADW 1QRTA 3AIIA 2HZ7A 5DM6S 4JXZA 3J7ZV 5JVGS 4H3SA 5GAEW 4WFAS 4IOAS 1FEUA 5IZNA 1ZJWA 4WF9S 4WFNS 2RD2A 4IOCS 4JXXA 5JVHS 2ZJRS 3CF5S 4P2BA 5BNZA 5GAHW 1EXDA 1GTSA 4UY88 2RE8A 1EUYA 5DM7S 4WCES 3PIPS 1NYLA 1QRUA 4U67S 1B75A 1QRSA 1QTQA 1DFUP 1GTRA 3PIOS 4JYZA 1D6KA 1EUQA
chains in the Genus database with same CATH superfamily
2AE0X 4IO9S 5HL7S 3X1LB 1I6VA 2NWAA 4AYBD 4C2MC 5D4DA 3HOVC 4LJZA 5IYBC 1O0BA 4Q5SA 3I4MC 3AIIA 2HZ7A 4BY7C 4A3DC 4XLPA 3J7ZV 2KXYA 3GTMC 5GAEW 4WFAS 3HOXC 5C3EC 4YFKA 2YU9C 3CZBA 2NVQC 1ZJWA 3HOUC 3S16C 2PMZD 2CW0A 2RD2A 4MEXA 1TWFC 2PI8A 2PNWA 4ZH4A 4OINA 3PO2C 2ZJRS 5GAHW 3GTJC 1YNNA 4BBRC 4G7ZA 5DM7S 4JK1A 4WCES 2A6EA 4A3JC 1QRUA 4E8BA 5C4XC 1QRSA 4MEYA 2E2HC 4Y52C 1TWGC 5IP7C 1VHKA 3HOZC 3H0GC 2ZJQS 3RZDC 4BY1C 3S1NC 4X6AC 4Y7NC 1UDXA 5GADW 5FLMC 4MQ9A 2L3UA 4YG2A 3S17C 4H4KA 2Z0YA 2R93C 3CQZC 3HKZD 3S15C 2PJJA 1BDFA 1V6ZA 1FEUA 2A6HA 4C3JC 5IZNA 4KN7A 2O5IA 2JA8C 4A93C 4WFNS 4IOCS 4XLNA 5TMCA 3DXJA 5IYDC 5JVHS 2B63C 1ZYRA 4UY88 3CF5S 4P2BA 4L69A 4LK0A 4YFXA 3EQLA 1WCMC 1I6HC 3FKIC 2JA7C 2A68A 3S1MC 1Y1VC 2NVXC 2E2JC 4A3MC 4JYZA 2GAEA 2BE5A 4G7HA 3DLLS 1SFOC 1HQMA 4OIRA 4YFNA 4OIPA 2A69A 2PPBA 2EGWA 1R9TC 1QRTA 2R92C 3I4NC 4BBSC 2G5DA 5DM6S 4JXZA 3M3YC 4H3SA 2NVTC 1I3QC 4C3HC 2VUMC 3PO3C 4A3GC 3GTGC 2JA6C 1TWHC 4A3EC 4A3BC 1Z85A 4QIWD 3HOWC 3GTPC 2KPUA 1GTSA 5BNZA 2Y0SD 3S14C 2RE8A 1EUYA 4J3CA 5IP9C 3HOYC 3GTQC 4OIQA 1NYLA 4BXXC 4V194 1B75A 3KW2A 1I50C 1K83C 2WB1D 1QTQA 3GTOC 1DFUP 4LLGA 4A3LC 2O5JA 1O0CA 2ZJPS 4KN4A 5C44C 1IW7A 1YNJA 5C4JC 3LYWA 4WFBS 2E2IC 3RZOC 3S1QC 3W2WB 1SMYA 2KQ1A 5GAGW 4NOIA 4A3IC 1Y1WC 2R7ZC 3M4OC 3GTKC 5HQHA 2EGVA 3K7AC 4A3KC 1TWAC 5JVGS 5IYCC 2PA8D 2NVYC 1VHYA 2PICA 4XSXA 4IOAS 4QJVA 4LK1A 3W2VB 4WF9S 4G7OA 2CX8A 3S1RC 5TMFA 4JXXA 4XSZA 1NXZA 1EXDA 4C3IC 1TWCC 4A3FC 3S2DC 4A3CC 2G6GA 2L5NA 2WAQD 3H3VD 3PIPS 3GTLC 3WODA 4U67S 3S2HC 4KMUA 4Q4ZA 4OIOA 1GTRA 2JA5C 3PIOS 4GZYA 1D6KA 1EUQA
chains in the Genus database with same CATH topology
1O0CA 2ZJPS 3DLLS 4IO9S 5HL7S 3X1LB 4WFBS 3W2WB 2ZJQS 5GAGW 1O0BA 1UDXA 5GADW 3AIIA 2HZ7A 1QRTA 5DM6S 4JXZA 4H4KA 3J7ZV 5JVGS 4H3SA 5GAEW 4WFAS 4IOAS 1FEUA 5IZNA 1ZJWA 3W2VB 4WFNS 4WF9S 2RD2A 4IOCS 4JXXA 5JVHS 2ZJRS 3CF5S 4P2BA 5BNZA 5GAHW 1EXDA 1GTSA 4UY88 2RE8A 1EUYA 5DM7S 4WCES 3PIPS 1NYLA 4V194 1QRUA 4U67S 1B75A 1QRSA 1QTQA 1DFUP 1GTRA 3PIOS 4JYZA 1D6KA 1EUQA
chains in the Genus database with same CATH homology


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