1D6KA

Nmr solution structure of the 5s rrna e-loop/l25 complex
Total Genus 22
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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
22
sequence length
94
structure length
94
Chain Sequence
MFTINAEVRKEQGKGASRRLRAANKFPAIIYGGKEAPLAIELDHDKVMNMQAKAEFYSEVLTIVVDGKEIKVKAQDVQRHPYKPKLQHIDFVRA
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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 5S RRNA E-LOOP (5SE)
publication title The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Ribosome
total genus 22
structure length 94
sequence length 94
ec nomenclature
pdb deposition date 1999-10-14

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF01386 Ribosomal_L25p Ribosomal L25p family
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 1d6kA00
4WFAS 5DM6S 1DFUP 1FEUA 1B75A 1EXDA 4H3SA 3PIOS 5GADW 4WCES 1GTRA 2RE8A 4UY88 3AIIA 3DLLS 4JYZA 5IZNA 2ZJQS 4P2BA 5GAEW 1EUYA 4IOAS 2ZJRS 1QRUA 5GAGW 3PIPS 1ZJWA 5DM7S 5HL7S 5JVGS 2ZJPS 4WFNS 4JXXA 3CF5S 1D6KA 1GTSA 3J7ZV 1QRSA 5JVHS 1O0BA 1QRTA 5GAHW 4U67S 1NYLA 4WF9S 4WFBS 2RD2A 4JXZA 2HZ7A 4IO9S 1O0CA 5BNZA 1QTQA 4IOCS 1EUQA
chains in the Genus database with same CATH superfamily
5DM6S 1DFUP 1EXDA 2PNWA 4UY88 2ZJQS 5GAEW 4V194 1QRUA 2ZJPS 1VHYA 4L69A 2EGWA 4J3CA 1D6KA 5JVHS 5GAHW 1NYLA 4WF9S 2G5DA 2RD2A 3X1LB 1EUQA 3KW2A 4H3SA 2PI8A 2RE8A 3W2VB 3DLLS 4JYZA 1EUYA 4IOAS 2ZJRS 1NXZA 3CF5S 1GTSA 3J7ZV 1QRTA 4WFBS 1Z85A 2HZ7A 4IOCS 4WFAS 2CX8A 1UDXA 1FEUA 2Z0YA 2EGVA 2G6GA 3CZBA 4H4KA 3AIIA 2AE0X 5IZNA 5GAGW 3PIPS 1ZJWA 5DM7S 4WFNS 4JXXA 1QRSA 1VHKA 4E8BA 4JXZA 1O0CA 1QTQA 1B75A 3PIOS 5GADW 4WCES 3W2WB 2GAEA 1GTRA 4P2BA 2PICA 5HL7S 5JVGS 2PJJA 1V6ZA 2NWAA 1O0BA 4U67S 4IO9S 5BNZA
chains in the Genus database with same CATH topology
4WFAS 5DM6S 1DFUP 1FEUA 1UDXA 1B75A 1EXDA 4H3SA 3PIOS 5GADW 4WCES 3W2WB 1GTRA 2RE8A 3W2VB 4H4KA 3AIIA 4UY88 3DLLS 4JYZA 5IZNA 2ZJQS 4P2BA 5GAEW 1EUYA 4V194 2ZJRS 1QRUA 5GAGW 3PIPS 4IOAS 1ZJWA 5DM7S 5HL7S 5JVGS 2ZJPS 4WFNS 4JXXA 3CF5S 1D6KA 1GTSA 3J7ZV 1QRSA 5JVHS 1O0BA 1QRTA 5GAHW 4U67S 1NYLA 4WF9S 4WFBS 2RD2A 4JXZA 2HZ7A 4IO9S 1O0CA 5BNZA 1QTQA 4IOCS 3X1LB 1EUQA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4WFA S;  5DM6 S;  1DFU P;  1FEU A;  1B75 A;  1EXD A;  4H3S A;  3PIO S;  5GAD W;  4WCE S;  1GTR A;  2RE8 A;  4UY8 8;  3AII A;  3DLL S;  4JYZ A;  5IZN A;  2ZJQ S;  4P2B A;  5GAE W;  1EUY A;  4IOA S;  2ZJR S;  1QRU A;  5GAG W;  3PIP S;  1ZJW A;  5DM7 S;  5HL7 S;  5JVG S;  2ZJP S;  4WFN S;  4JXX A;  3CF5 S;  1D6K A;  1GTS A;  3J7Z V;  1QRS A;  5JVH S;  1O0B A;  1QRT A;  5GAH W;  4U67 S;  1NYL A;  4WF9 S;  4WFB S;  2RD2 A;  4JXZ A;  2HZ7 A;  4IO9 S;  1O0C A;  5BNZ A;  1QTQ A;  4IOC S;  1EUQ A; 
#chains in the Genus database with same CATH topology
 5DM6 S;  1DFU P;  1EXD A;  2PNW A;  4UY8 8;  2ZJQ S;  5GAE W;  4V19 4;  1QRU A;  2ZJP S;  1VHY A;  4L69 A;  2EGW A;  4J3C A;  1D6K A;  5JVH S;  5GAH W;  1NYL A;  4WF9 S;  2G5D A;  2RD2 A;  3X1L B;  1EUQ A;  3KW2 A;  4H3S A;  2PI8 A;  2RE8 A;  3W2V B;  3DLL S;  4JYZ A;  1EUY A;  4IOA S;  2ZJR S;  1NXZ A;  3CF5 S;  1GTS A;  3J7Z V;  1QRT A;  4WFB S;  1Z85 A;  2HZ7 A;  4IOC S;  4WFA S;  2CX8 A;  1UDX A;  1FEU A;  2Z0Y A;  2EGV A;  2G6G A;  3CZB A;  4H4K A;  3AII A;  2AE0 X;  5IZN A;  5GAG W;  3PIP S;  1ZJW A;  5DM7 S;  4WFN S;  4JXX A;  1QRS A;  1VHK A;  4E8B A;  4JXZ A;  1O0C A;  1QTQ A;  1B75 A;  3PIO S;  5GAD W;  4WCE S;  3W2W B;  2GAE A;  1GTR A;  4P2B A;  2PIC A;  5HL7 S;  5JVG S;  2PJJ A;  1V6Z A;  2NWA A;  1O0B A;  4U67 S;  4IO9 S;  5BNZ A; 
#chains in the Genus database with same CATH homology
 4WFA S;  5DM6 S;  1DFU P;  1FEU A;  1UDX A;  1B75 A;  1EXD A;  4H3S A;  3PIO S;  5GAD W;  4WCE S;  3W2W B;  1GTR A;  2RE8 A;  3W2V B;  4H4K A;  3AII A;  4UY8 8;  3DLL S;  4JYZ A;  5IZN A;  2ZJQ S;  4P2B A;  5GAE W;  1EUY A;  4V19 4;  2ZJR S;  1QRU A;  5GAG W;  3PIP S;  4IOA S;  1ZJW A;  5DM7 S;  5HL7 S;  5JVG S;  2ZJP S;  4WFN S;  4JXX A;  3CF5 S;  1D6K A;  1GTS A;  3J7Z V;  1QRS A;  5JVH S;  1O0B A;  1QRT A;  5GAH W;  4U67 S;  1NYL A;  4WF9 S;  4WFB S;  2RD2 A;  4JXZ A;  2HZ7 A;  4IO9 S;  1O0C A;  5BNZ A;  1QTQ A;  4IOC S;  3X1L B;  1EUQ 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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