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


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