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


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