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
publication title Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A.
pubmed doi rcsb
molecule keywords 50S ribosomal protein L1
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
2ZJRS 1EXDA 5GAEW 3CF5S 3AIIA 1QRUA 1ZJWA 1FEUA 4WFAS 1B75A 5JVHS 5JVGS 1NYLA 4WCES 4JYZA 3DLLS 3PIOS 4UY88 1O0CA 4WFNS 4H3SA 3J7ZV 1D6KA 5BNZA 4WFBS 1QRSA 3PIPS 4JXXA 5GADW 1QRTA 4U67S 4IOAS 2ZJPS 2ZJQS 1O0BA 4P2BA 2RE8A 1GTRA 5GAGW 5DM6S 4IO9S 1EUYA 4WF9S 4IOCS 2HZ7A 5DM7S 4JXZA 2RD2A 5GAHW 1QTQA 5IZNA 1DFUP 5HL7S 1GTSA 1EUQA
chains in the Genus database with same CATH superfamily
3GTPC 1EXDA 3W2VB 2R92C 5GAEW 3CF5S 4Q5SA 4A3GC 3K7AC 4QJVA 4AYBD 2CX8A 1NXZA 2Z0YA 2JA8C 5TMFA 5IYBC 5JVHS 1TWHC 3S1MC 4BXXC 4JK1A 1NYLA 3S1RC 3HOUC 2PPBA 4Y52C 4XLPA 3HOZC 2L5NA 3S17C 4UY88 4A3DC 4WFNS 4X6AC 5IP9C 5BNZA 4WFBS 4A3BC 2NWAA 3PIPS 3GTGC 3PO2C 5GADW 1QRTA 2NVTC 4BBSC 2JA5C 4YFKA 5C4JC 4A3FC 2ZJQS 1I6VA 4P2BA 3H3VD 2GAEA 4A3EC 4A3MC 5DM6S 3H0GC 4OIOA 1Z85A 3S1NC 1TWGC 2CW0A 5IZNA 2Y0SD 2G6GA 1YNNA 5IYDC 3M3YC 4NOIA 3GTMC 3HOWC 3X1LB 4XLNA 1ZJWA 1VHYA 4OIPA 2PICA 5JVGS 3DXJA 1Y1WC 4E8BA 2JA7C 1Y1VC 2PNWA 4WCES 4A3LC 3DLLS 3GTOC 4G7HA 2VUMC 2KXYA 2NVXC 4MEYA 1I6HC 4V194 2KPUA 3J7ZV 2EGVA 4YFNA 4C3IC 4Y7NC 1QRSA 3I4MC 3S16C 2R7ZC 4IOAS 3FKIC 3S15C 3I4NC 2ZJPS 4LK1A 3HOXC 3CQZC 3GTJC 2PJJA 2A68A 4KN7A 1SFOC 4BY7C 5GAGW 4IO9S 4WF9S 1EUYA 4MEXA 4OIQA 3HOYC 4A3CC 2A69A 5DM7S 5C44C 2RD2A 5GAHW 1QTQA 1TWFC 1WCMC 1EUQA 2PMZD 1R9TC 2E2IC 1QRUA 3GTQC 2A6EA 1FEUA 2KQ1A 2L3UA 2NVQC 4WFAS 4YG2A 5D4DA 4C3JC 3M4OC 5C3EC 4JYZA 1TWCC 4H4KA 2YU9C 3S14C 4BBRC 5IP7C 4LLGA 3PIOS 2G5DA 2NVYC 4XSXA 5TMCA 4H3SA 4ZH4A 4C2MC 4L69A 3PO3C 4A93C 4JXXA 3KW2A 4U67S 3S1QC 5HQHA 2E2HC 1I3QC 4MQ9A 3CZBA 3EQLA 3WODA 2RE8A 2AE0X 3RZDC 1TWAC 2EGWA 1K83C 4IOCS 2PI8A 1VHKA 4JXZA 2WB1D 4KN4A 1DFUP 3GTKC 1B75A 5HL7S 3LYWA 2R93C 2ZJRS 3W2WB 3AIIA 2O5IA 2A6HA 4LK0A 4OIRA 4C3HC 1YNJA 1SMYA 1HQMA 4XSZA 4GZYA 2WAQD 2JA6C 4A3KC 4BY1C 4A3IC 4QIWD 4OINA 1ZYRA 4LJZA 1O0CA 1D6KA 4YFXA 5IYCC 4KMUA 2B63C 4G7ZA 2E2JC 3RZOC 1UDXA 1IW7A 1V6ZA 1BDFA 3S2DC 1O0BA 4A3JC 2O5JA 3GTLC 1GTRA 3S2HC 2BE5A 3HKZD 2HZ7A 4J3CA 4Q4ZA 1I50C 5FLMC 5C4XC 3HOVC 4G7OA 2PA8D 1GTSA
chains in the Genus database with same CATH topology
2ZJRS 3W2WB 1EXDA 3W2VB 5GAEW 3CF5S 3AIIA 1QRUA 3X1LB 1ZJWA 1FEUA 4WFAS 1B75A 5JVHS 5JVGS 1NYLA 4WCES 4JYZA 4H4KA 3DLLS 3PIOS 4UY88 1O0CA 4WFNS 4H3SA 3J7ZV 1D6KA 5BNZA 4V194 4WFBS 1QRSA 3PIPS 4JXXA 5GADW 1QRTA 4U67S 4IOAS 1UDXA 2ZJPS 2ZJQS 1O0BA 4P2BA 2RE8A 1GTRA 5GAGW 5DM6S 4IO9S 1EUYA 4WF9S 4IOCS 2HZ7A 5DM7S 4JXZA 2RD2A 5GAHW 1QTQA 5IZNA 1DFUP 5HL7S 1GTSA 1EUQA
chains in the Genus database with same CATH homology


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