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


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

 
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#similar chains, but unknotted
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