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


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