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


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