5DM7S

Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans in complex with hygromycin a
Total Genus 19
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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
19
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 19
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 5dm7S01
2.170.120.20 Mainly Beta Beta Complex RNA Polymerase Alpha Subunit; Chain A, domain 2 Ribosomal protein L25, beta domain 5dm7S02
3CF5S 2RE8A 2ZJPS 5JVGS 5DM6S 5GAGW 1GTRA 4WFBS 4WFAS 4P2BA 1QRTA 1DFUP 1EUQA 5JVHS 1EXDA 2HZ7A 1O0BA 4WF9S 3AIIA 1NYLA 4U67S 2ZJQS 2RD2A 4JYZA 1QRUA 4IOAS 5BNZA 5DM7S 1D6KA 4JXXA 5HL7S 1ZJWA 1O0CA 3PIPS 4UY88 5GAHW 5GAEW 1QTQA 4JXZA 1EUYA 5IZNA 3PIOS 5GADW 1FEUA 3DLLS 4IOCS 1GTSA 1QRSA 2ZJRS 4IO9S 4WCES 4H3SA 1B75A 4WFNS 3J7ZV
chains in the Genus database with same CATH superfamily
3CF5S 3GTMC 1K83C 1GTRA 2L5NA 4A3EC 1QRTA 2PNWA 3HOWC 4A3KC 1EUQA 1TWGC 1YNNA 3S1NC 4YFKA 5HQHA 4NOIA 4WF9S 3RZDC 3GTKC 3S15C 4IOAS 5BNZA 4KN4A 4YFNA 5DM7S 4BXXC 2E2HC 3H0GC 4QIWD 5GAHW 3GTOC 4XSXA 4GZYA 2WAQD 1I6VA 1QRSA 2A6HA 3H3VD 2R93C 4H3SA 4BBSC 2PI8A 2L3UA 1IW7A 3HOYC 2NVTC 1ZYRA 3M3YC 1TWFC 1SMYA 1I3QC 5JVGS 4LK0A 4AYBD 3RZOC 3S17C 4XLNA 4Q5SA 5GAGW 3S2HC 4WFBS 2NWAA 4V194 3GTPC 1O0BA 2O5IA 3AIIA 3GTJC 2AE0X 3S16C 2BE5A 2KPUA 4OIOA 4OIRA 2NVQC 1Y1VC 1NXZA 1ZJWA 2O5JA 4H4KA 1UDXA 3PO2C 2G6GA 4L69A 4KN7A 5IZNA 4LK1A 2NVYC 3DLLS 1TWCC 5TMFA 4Y52C 1HQMA 4A3LC 2JA7C 1Z85A 1GTSA 2CW0A 2WB1D 4QJVA 3LYWA 4JK1A 1VHYA 4Q4ZA 2JA5C 5IYCC 4OIQA 3M4OC 4A3CC 3WODA 3PO3C 2Z0YA 2E2JC 4C2MC 2B63C 4LJZA 4WFAS 4P2BA 5C44C 1DFUP 4A3IC 2CX8A 3EQLA 4C3IC 2HZ7A 2R92C 3HOXC 4OINA 1I50C 1NYLA 4U67S 1QRUA 1Y1WC 5IP7C 5IYBC 3S1RC 3HOVC 4A3DC 1TWAC 1D6KA 4A3BC 4JXXA 4J3CA 4JXZA 3PIPS 1WCMC 4XSZA 2PA8D 3GTQC 3S2DC 4A3MC 3GTLC 3PIOS 5GADW 1FEUA 2JA8C 2G5DA 4X6AC 2A6EA 4IOCS 2VUMC 4LLGA 3S14C 4WCES 4XLPA 4G7HA 5TMCA 4Y7NC 4G7ZA 4A3FC 1VHKA 4YG2A 1TWHC 2A68A 4BY1C 4G7OA 4A3JC 3I4MC 2KXYA 3HOZC 5FLMC 1B75A 4KMUA 1YNJA 4WFNS 2PMZD 3J7ZV 2PPBA 2RE8A 2ZJPS 3K7AC 4A93C 3W2WB 5DM6S 2JA6C 2PJJA 3KW2A 3DXJA 5IP9C 5C4JC 2Y0SD 2YU9C 4MEXA 5JVHS 1EXDA 5IYDC 4E8BA 2ZJQS 4JYZA 3CQZC 4A3GC 2RD2A 3HKZD 4BBRC 1R9TC 3FKIC 2PICA 4ZH4A 1V6ZA 4MEYA 2R7ZC 3I4NC 1O0CA 5HL7S 4UY88 5GAEW 1QTQA 3S1QC 1SFOC 3W2VB 1EUYA 4C3JC 3CZBA 4C3HC 2NVXC 1I6HC 4BY7C 2ZJRS 4IO9S 4OIPA 3HOUC 4YFXA 5C3EC 5C4XC 2EGWA 1BDFA 4MQ9A 3X1LB 2EGVA 5D4DA 3S1MC 2GAEA 2KQ1A 3GTGC 2E2IC 2A69A
chains in the Genus database with same CATH topology
3CF5S 2RE8A 2ZJPS 5JVGS 3W2WB 5DM6S 5GAGW 1GTRA 4WFBS 4WFAS 4V194 4P2BA 1QRTA 1DFUP 1EUQA 5JVHS 1EXDA 2HZ7A 1O0BA 4WF9S 3AIIA 1NYLA 4U67S 2ZJQS 2RD2A 4JYZA 1QRUA 4IOAS 5BNZA 5DM7S 1D6KA 4JXXA 5HL7S 1ZJWA 1O0CA 3PIPS 4H4KA 1UDXA 5GAEW 5GAHW 4UY88 1QTQA 4JXZA 3W2VB 1EUYA 5IZNA 3PIOS 5GADW 1FEUA 3DLLS 4IOCS 1GTSA 1QRSA 2ZJRS 4IO9S 4WCES 4H3SA 3X1LB 1B75A 4WFNS 3J7ZV
chains in the Genus database with same CATH homology


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