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
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 Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
pubmed doi rcsb
molecule tags Ribosome
molecule keywords 50S ribosomal protein L1
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
2ZJQS 2RE8A 5JVGS 1B75A 4WF9S 3PIOS 1QRTA 1EXDA 2ZJRS 1O0CA 3AIIA 1NYLA 5GADW 2RD2A 1GTSA 4U67S 4WFBS 3J7ZV 4WCES 4IO9S 5DM6S 1D6KA 5GAEW 4H3SA 5GAHW 4IOCS 1QRUA 1ZJWA 1O0BA 3PIPS 2ZJPS 1EUYA 1DFUP 5GAGW 3CF5S 4WFNS 4JXZA 1FEUA 5HL7S 5BNZA 3DLLS 4WFAS 1GTRA 2HZ7A 1QRSA 1QTQA 5DM7S 4IOAS 4P2BA 4JYZA 1EUQA 5JVHS 4UY88 5IZNA 4JXXA
chains in the Genus database with same CATH superfamily
2EGWA 5JVGS 1TWHC 2JA5C 3S1RC 1QRTA 2AE0X 2BE5A 3EQLA 4C3IC 1SFOC 4BY1C 3K7AC 4A3MC 4IO9S 3HOWC 4MEYA 4WCES 1HQMA 5DM6S 5IYBC 1D6KA 5GAEW 4YG2A 3S16C 3HOYC 3S15C 2NWAA 1O0BA 2E2JC 2YU9C 1IW7A 4A3JC 5TMFA 4QJVA 3S14C 1EUYA 1TWCC 4BXXC 4A3LC 4YFNA 5HQHA 4LK1A 5IYDC 4Q5SA 4H4KA 1QRSA 2PPBA 3S2DC 3HKZD 2JA7C 2PJJA 4JYZA 4NOIA 4A3EC 2PA8D 1SMYA 4JXZA 2E2IC 4KN4A 1NXZA 2CX8A 4MQ9A 2CW0A 3CQZC 3PIOS 4JK1A 1EXDA 2ZJRS 3LYWA 4J3CA 2Z0YA 1Y1VC 3AIIA 1NYLA 2NVXC 4GZYA 4WFBS 4E8BA 4BY7C 4V194 2PNWA 4BBRC 4H3SA 5GAHW 3HOXC 2NVTC 3PO3C 5IP9C 3S1NC 1YNJA 2G6GA 1I50C 2A68A 4OIPA 3PIPS 2ZJPS 2NVQC 3W2VB 4LLGA 2KQ1A 4C3HC 3RZDC 4WFAS 5IYCC 4XLNA 3H0GC 2R92C 2L3UA 4OIOA 3GTKC 2O5JA 3S1QC 5DM7S 2PICA 4XLPA 2A6EA 5C3EC 4UY88 5IZNA 4JXXA 2A6HA 3S2HC 3GTOC 1UDXA 2ZJQS 1B75A 2PMZD 1TWFC 4WF9S 2E2HC 2GAEA 1O0CA 5GADW 2RD2A 1GTSA 1VHYA 3S1MC 3DXJA 3GTGC 1R9TC 3CZBA 3H3VD 4IOCS 4XSZA 3GTLC 5D4DA 2O5IA 4A3GC 5TMCA 3GTQC 1ZJWA 4ZH4A 4Y7NC 4A3CC 4A3IC 5IP7C 4X6AC 3M4OC 1DFUP 1ZYRA 2G5DA 4Y52C 4A3DC 1I3QC 4G7OA 1TWGC 2B63C 5HL7S 1GTRA 4A3FC 4MEXA 4OIQA 2HZ7A 3X1LB 3RZOC 3S17C 4BBSC 2A69A 2NVYC 5FLMC 4QIWD 4IOAS 4G7HA 4P2BA 1EUQA 5C4XC 1YNNA 5JVHS 3GTJC 3W2WB 2RE8A 1I6VA 2KPUA 1Y1WC 1K83C 4C2MC 3I4MC 2WAQD 4LK0A 4OIRA 2KXYA 3GTPC 3PO2C 4L69A 2R7ZC 4Q4ZA 4U67S 3J7ZV 2PI8A 1VHKA 1TWAC 2EGVA 4YFKA 3HOZC 4KMUA 1Z85A 4A3BC 4LJZA 4OINA 2VUMC 1QRUA 1V6ZA 4A3KC 3HOUC 4A93C 2L5NA 3I4NC 4AYBD 5C44C 5GAGW 2JA6C 3CF5S 4WFNS 1FEUA 3FKIC 4C3JC 1BDFA 2WB1D 5BNZA 3DLLS 1QTQA 3GTMC 3WODA 3HOVC 1I6HC 4XSXA 4YFXA 5C4JC 2JA8C 4KN7A 2Y0SD 3M3YC 2R93C 3KW2A 1WCMC 4G7ZA
chains in the Genus database with same CATH topology
1UDXA 3W2WB 2ZJQS 2RE8A 5JVGS 4WF9S 3PIOS 1QRTA 1B75A 1EXDA 2ZJRS 1O0CA 3AIIA 1NYLA 5GADW 2RD2A 1GTSA 4U67S 4WFBS 3J7ZV 4WCES 4IO9S 5DM6S 4V194 1D6KA 5GAEW 4H3SA 5GAHW 4IOCS 1QRUA 1ZJWA 1O0BA 3PIPS 2ZJPS 3W2VB 1EUYA 1DFUP 5GAGW 3CF5S 4WFNS 4JXZA 1FEUA 5HL7S 5BNZA 3DLLS 4H4KA 4WFAS 2HZ7A 1GTRA 1QRSA 1QTQA 3X1LB 5DM7S 4IOAS 4P2BA 4JYZA 1EUQA 5JVHS 4UY88 5IZNA 4JXXA
chains in the Genus database with same CATH homology


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