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


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