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


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