1DFUP

Crystal structure of e.coli ribosomal protein l25 complexed with a 5s rrna fragment at 1.8 a resolution
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
publication title Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution.
pubmed doi rcsb
source organism Escherichia coli
molecule tags Ribosome
total genus 22
structure length 94
sequence length 94
ec nomenclature
pdb deposition date 1999-11-21

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
P 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 1dfuP00
1QRUA 1EXDA 3CF5S 5JVHS 1EUQA 5GADW 5IZNA 1O0BA 1QRTA 1QTQA 2ZJPS 1GTSA 4IOAS 4WFBS 5GAGW 2ZJQS 1B75A 1DFUP 1O0CA 3PIOS 4IO9S 1GTRA 2RE8A 5GAHW 2RD2A 2ZJRS 4IOCS 4WCES 1NYLA 3PIPS 4H3SA 4JYZA 4JXZA 5GAEW 4WF9S 5BNZA 1EUYA 4P2BA 4U67S 5DM6S 5JVGS 4JXXA 4UY88 4WFNS 1QRSA 1ZJWA 3J7ZV 5DM7S 5HL7S 4WFAS 3AIIA 2HZ7A 1D6KA 3DLLS 1FEUA
chains in the Genus database with same CATH superfamily
3CF5S 1QTQA 2PI8A 1Z85A 1GTRA 2GAEA 2AE0X 3PIPS 2NWAA 4JYZA 5GAEW 5BNZA 4P2BA 5JVGS 3J7ZV 3W2VB 5HL7S 1D6KA 1QRUA 4E8BA 1EXDA 5JVHS 5GADW 5IZNA 4H4KA 3KW2A 2ZJPS 4WFBS 1VHYA 2ZJQS 1B75A 1DFUP 4IO9S 3CZBA 1NXZA 4V194 4J3CA 1EUYA 4U67S 3W2WB 4WFAS 3AIIA 2HZ7A 2ZJRS 3DLLS 1O0BA 1GTSA 1UDXA 2CX8A 2G5DA 5GAHW 2RD2A 4IOCS 1NYLA 5DM6S 4UY88 2EGVA 1QRSA 1ZJWA 5DM7S 2PNWA 1FEUA 4L69A 1QRTA 1EUQA 2G6GA 4IOAS 5GAGW 1O0CA 3PIOS 2RE8A 2PICA 4WCES 2PJJA 3X1LB 4H3SA 1V6ZA 4JXZA 2Z0YA 4WF9S 4JXXA 4WFNS 1VHKA 2EGWA
chains in the Genus database with same CATH topology
1QRUA 1EXDA 3CF5S 5JVHS 1EUQA 5GADW 5IZNA 4H4KA 1O0BA 1QRTA 1QTQA 2ZJPS 1GTSA 4IOAS 4WFBS 5GAGW 1UDXA 2ZJQS 1B75A 1DFUP 1O0CA 3PIOS 4IO9S 1GTRA 2RE8A 5GAHW 2RD2A 2ZJRS 4IOCS 4WCES 3X1LB 1NYLA 3PIPS 4H3SA 4V194 4JYZA 4JXZA 5GAEW 4WF9S 5BNZA 1EUYA 4P2BA 4U67S 3W2WB 5DM6S 5JVGS 4JXXA 4WFNS 4UY88 1QRSA 1ZJWA 3J7ZV 5DM7S 3W2VB 5HL7S 4WFAS 3AIIA 2HZ7A 1D6KA 3DLLS 1FEUA
chains in the Genus database with same CATH homology


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