5IZNA

The crystal structure of 50s ribosomal protein l25 from vibrio vulnificus cmcp6
Total Genus 10
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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
10
sequence length
94
structure length
94
Chain Sequence
NAMKFEAVVRTELGKGASRRLRLAGQFPAVVYGGEAAPVAVALNHDDIVNQMDKPEFYEAITLVIGGEEVKVKPQDVQRHAFKPKVEHMDFIRI
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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 tags Ribosomal protein
molecule keywords 50S ribosomal protein L25
publication title The crystal structure of 50S ribosomal protein L25 from Vibrio vulnificus CMCP6
rcsb
source organism Vibrio vulnificus (strain cmcp6)
total genus 10
structure length 94
sequence length 94
chains with identical sequence B, C, D, E, F, G, H
ec nomenclature
pdb deposition date 2016-03-25

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A 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 5iznA00
3J7ZV 2ZJRS 4WFBS 1EXDA 1O0CA 4WFAS 5BNZA 5DM7S 4UY88 1QRTA 3CF5S 1EUQA 1QRUA 5JVHS 4WFNS 4IOAS 1GTRA 4JXZA 5GAEW 1FEUA 1DFUP 1GTSA 2HZ7A 3AIIA 2RD2A 5GADW 1D6KA 1B75A 1EUYA 4P2BA 3PIOS 2ZJPS 5JVGS 1O0BA 1QTQA 4WF9S 5GAGW 4JYZA 4IOCS 4JXXA 3DLLS 1NYLA 2ZJQS 1ZJWA 4WCES 5DM6S 4IO9S 3PIPS 4U67S 1QRSA 5IZNA 5HL7S 4H3SA 2RE8A 5GAHW
chains in the Genus database with same CATH superfamily
2ZJRS 4WFBS 4E8BA 1QRTA 3KW2A 5JVHS 2PJJA 4WFNS 4IOAS 1GTRA 3W2VB 2PI8A 2HZ7A 1VHYA 2RD2A 2PICA 1Z85A 4IOCS 4WCES 4IO9S 2G6GA 2EGVA 1O0CA 4WFAS 5DM7S 3CF5S 1EUQA 1VHKA 4JXZA 3CZBA 1GTSA 4P2BA 3PIOS 2ZJPS 4JXXA 3DLLS 1NYLA 2AE0X 3PIPS 4U67S 1QRSA 2EGWA 4H3SA 1EXDA 2GAEA 1NXZA 5GAEW 3AIIA 1B75A 5GADW 1EUYA 2NWAA 5JVGS 1QTQA 4WF9S 5GAGW 3W2WB 1ZJWA 5IZNA 5HL7S 4V194 2PNWA 2RE8A 5GAHW 3J7ZV 5BNZA 4UY88 4H4KA 4J3CA 1QRUA 1V6ZA 2G5DA 1FEUA 1DFUP 4L69A 1D6KA 1O0BA 2Z0YA 4JYZA 1UDXA 3X1LB 2ZJQS 2CX8A 5DM6S
chains in the Genus database with same CATH topology
3J7ZV 2ZJRS 4WFBS 1EXDA 1O0CA 4WFAS 5BNZA 5DM7S 4UY88 4H4KA 1QRTA 3CF5S 1EUQA 1QRUA 5JVHS 4WFNS 4IOAS 1GTRA 4JXZA 3W2VB 5GAEW 1FEUA 1DFUP 1GTSA 2HZ7A 3AIIA 2RD2A 5GADW 1D6KA 1B75A 1EUYA 4P2BA 3PIOS 2ZJPS 5JVGS 1O0BA 1QTQA 4WF9S 5GAGW 4JYZA 4IOCS 4JXXA 3DLLS 1NYLA 1UDXA 3X1LB 3W2WB 2ZJQS 1ZJWA 5DM6S 4WCES 4IO9S 3PIPS 4U67S 1QRSA 5IZNA 5HL7S 4H3SA 4V194 2RE8A 5GAHW
chains in the Genus database with same CATH homology


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