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


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

 
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#similar chains, but unknotted
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