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


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