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


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