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


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