5DM6S

Crystal structure of the 50s ribosomal subunit from deinococcus radiodurans
Total Genus 22
Loading diagram...

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
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...