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


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