3KW2A

Crystal structure of probable rrna-methyltransferase from porphyromonas gingivalis
Total Genus 70
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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
70
Knots found
sequence length
245
structure length
240
Chain Sequence
LPLFYAPDIEQSDRLPDDEAGHILRVLRMQAGDRLRLTDGRGSFFDAVIETADRKSCYVSVCGQESWQKPWRDRITIAIAPTKQSERMEWMLEKLVEIGVDEVVFIESEHSERRRIKAERLERIAISAMKQSLKASFPVIRVNIPIQTVIADTPKAAVRLIAYVDEAVRGRGYPSDFYHVGQDVLILIGPEGDFSPSEVESALLAGFAPVSLGESRLRTETAGLVACQWIHTLQACYRIG
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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 Probable r-RNA methyltransferase
publication title Crystal structure of probable rRNA-methyltransferase from Porphyromonas gingivalis
rcsb
source organism Porphyromonas gingivalis atcc 33277
molecule tags Transferase
total genus 70
structure length 240
sequence length 245
chains with identical sequence B
other databases KnotProt 2.0: K +31
ec nomenclature
pdb deposition date 2009-11-30

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF04452 Methyltrans_RNA RNA methyltransferase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.240.20 Mainly Beta Beta Barrel Ribosomal Protein L25; Chain P Hypothetical PUA domain-like; domain 1 3kw2A01
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 3kw2A02
1K3RA 5GMBA 1V6ZA 1ZJRA 4YQ2A 3L8UA 4KDZA 4YQ3A 4YQKA 3NK6A 3E5YA 2Z0YA 4E8BA 2EGWA 1GZ0A 4YPYA 4X3LA 1Z85A 4YQBA 4YQJA 2EGVA 1O6DA 4JALA 4YQCA 3OIJA 4YPWA 3KTYA 4YQAA 4FAKA 3GYQA 3OIIA 4YQ8A 4KGNA 4YQGA 3ONPA 4MCCA 3N4JA 3N4KA 5CO4A 2HA8A 1VHKA 4YQ7A 1X7OA 3KNUA 4XBOA 4YQPA 1UAJA 5FAIA 4PZKA 4H3ZA 3BBEA 3IEFA 3OINA 4YVHA 1VH0A 1UAKA 4MCBA 2V3JA 4YQQA 4RG1A 4IG6A 1UALA 4YVIA 1NS5A 4CNGA 3NK7A 3AIAA 3AI9X 1TO0A 4YPZA 5D9FA 3DCMX 4YQDA 1V2XA 5GMCA 4YQLA 4YQ4A 4YQ5A 1IPAA 3KW2A 2I6DA 4YQRA 1NXZA 4JAKA 4X3MA 1P9PA 2YY8A 2NWAA 2QMMA 4YVJA 4YQNA 5GM8A 1VHYA 4YQOA 1UAMA 3KY7A 4YQSA 4YQIA 3BBDA 2QWVA 1OY5A 3O7BA 4CNFA 1MXIA 4MCDA 4YVKA 3QUVA 4H3YA 2V3KA 4YQ0A 4YQ1A 4YPXA 4L69A 4YVGA 3BBHA 4J3CA 1J85A 2CX8A 3ILKA 4CNEA 3IC6A 4YQ6A 2O3AA 4YQ9A 1X7PA 3AXZA 4YQTA 4CNDA
chains in the Genus database with same CATH superfamily
5DM7S 1K3RA 5GMBA 3AIIA 5JVHS 5GAEW 1V6ZA 1D6KA 1ZJRA 4YQ2A 3L8UA 1O0BA 4V194 4KDZA 4YQKA 3NK6A 4YQ3A 3W2VB 4U67S 3E5YA 1UDXA 5IZNA 2Z0YA 2ZJQS 2EGWA 4E8BA 1GZ0A 4YPYA 4X3LA 3PIOS 1Z85A 3PIPS 4YQBA 4YQJA 2EGVA 1O6DA 4JALA 4YQCA 3OIJA 4YPWA 3KTYA 4YQAA 4FAKA 3GYQA 3W2WB 2PNWA 4JXZA 3OIIA 4YQ8A 4KGNA 5HL7S 4IO9S 4YQGA 1EUQA 3ONPA 4JXXA 2HZ7A 5BNZA 3N4JA 4MCCA 4IOCS 4H4KA 3N4KA 5CO4A 2HA8A 1VHKA 5GAGW 4YQ7A 2ZJRS 1X7OA 2GAEA 3KNUA 4XBOA 4YQPA 1UAJA 5FAIA 4PZKA 4FMWA 4H3ZA 3CZBA 3X1LB 2ZJPS 3CF5S 3BBEA 3IEFA 3OINA 4YVHA 4UY88 1VH0A 1UAKA 4MCBA 1DFUP 2V3JA 4JWGA 4YQQA 4RG1A 4IG6A 1UALA 4YVIA 1NS5A 4CNGA 3NK7A 3AIAA 3AI9X 1TO0A 4YPZA 5D9FA 3DCMX 4YQDA 4WFAS 1V2XA 1ZJWA 5GMCA 4YQLA 1QRTA 4JWHA 3DLLS 2G6GA 4YQ4A 4YQ5A 1IPAA 3KW2A 4JWJA 4P2BA 2RE8A 2I6DA 4YQRA 1NXZA 2PJJA 2AE0X 1B75A 2RD2A 4IOAS 4JAKA 1QRSA 5GAHW 4X3MA 1P9PA 1GTRA 2YY8A 2NWAA 2QMMA 4YVJA 2PICA 4H3SA 4YQNA 5GM8A 3J7ZV 1VHYA 4YQOA 1UAMA 1NYLA 3KY7A 4YQSA 5GADW 4YQIA 3BBDA 2QWVA 1OY5A 3O7BA 4JWFA 5DM6S 4CNFA 1QRUA 4WF9S 1MXIA 4MCDA 4YVKA 3QUVA 4H3YA 4WFNS 2PI8A 4JYZA 1GTSA 5JVGS 1EUYA 2V3KA 1O0CA 1QTQA 1EXDA 4WCES 4YQ0A 4YQ1A 4YPXA 4L69A 4YVGA 3BBHA 4J3CA 1J85A 2CX8A 3ILKA 4CNEA 3IC6A 1FEUA 4YQ6A 2O3AA 4YQ9A 4WFBS 1X7PA 3AXZA 2G5DA 4YQTA 4CNDA
chains in the Genus database with same CATH topology
1K3RA 5GMBA 1V6ZA 1ZJRA 4YQ2A 3L8UA 4KDZA 4YQ3A 4YQKA 3NK6A 3E5YA 2Z0YA 4E8BA 2EGWA 1GZ0A 4YPYA 4X3LA 1Z85A 4YQBA 4YQJA 2EGVA 1O6DA 4JALA 4YQCA 3OIJA 4YPWA 3KTYA 4YQAA 4FAKA 3GYQA 3OIIA 4YQ8A 4KGNA 4YQGA 3ONPA 3N4JA 4MCCA 3N4KA 5CO4A 2HA8A 1VHKA 4YQ7A 1X7OA 3KNUA 4XBOA 4YQPA 1UAJA 5FAIA 4PZKA 4FMWA 4H3ZA 3BBEA 3IEFA 3OINA 4YVHA 1VH0A 1UAKA 4MCBA 2V3JA 4JWGA 4YQQA 4RG1A 4IG6A 1UALA 4YVIA 1NS5A 4CNGA 3NK7A 3AIAA 3AI9X 1TO0A 4YPZA 5D9FA 3DCMX 4YQDA 1V2XA 5GMCA 4YQLA 4JWHA 4YQ4A 4YQ5A 1IPAA 3KW2A 4JWJA 2I6DA 4YQRA 1NXZA 4JAKA 4X3MA 1P9PA 2YY8A 2NWAA 2QMMA 4YVJA 4YQNA 5GM8A 1VHYA 4YQOA 1UAMA 3KY7A 4YQSA 4YQIA 3BBDA 2QWVA 1OY5A 3O7BA 4JWFA 4CNFA 1MXIA 4MCDA 4YVKA 3QUVA 4H3YA 2V3KA 4YQ0A 4YQ1A 4YPXA 4L69A 4YVGA 3BBHA 4J3CA 1J85A 2CX8A 3ILKA 4CNEA 3IC6A 4YQ6A 2O3AA 4YQ9A 1X7PA 3AXZA 4YQTA 4CNDA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1K3R A;  5GMB A;  1V6Z A;  1ZJR A;  4YQ2 A;  3L8U A;  4KDZ A;  4YQ3 A;  4YQK A;  3NK6 A;  3E5Y A;  2Z0Y A;  4E8B A;  2EGW A;  1GZ0 A;  4YPY A;  4X3L A;  1Z85 A;  4YQB A;  4YQJ A;  2EGV A;  1O6D A;  4JAL A;  4YQC A;  3OIJ A;  4YPW A;  3KTY A;  4YQA A;  4FAK A;  3GYQ A;  3OII A;  4YQ8 A;  4KGN A;  4YQG A;  3ONP A;  4MCC A;  3N4J A;  3N4K A;  5CO4 A;  2HA8 A;  1VHK A;  4YQ7 A;  1X7O A;  3KNU A;  4XBO A;  4YQP A;  1UAJ A;  5FAI A;  4PZK A;  4H3Z A;  3BBE A;  3IEF A;  3OIN A;  4YVH A;  1VH0 A;  1UAK A;  4MCB A;  2V3J A;  4YQQ A;  4RG1 A;  4IG6 A;  1UAL A;  4YVI A;  1NS5 A;  4CNG A;  3NK7 A;  3AIA A;  3AI9 X;  1TO0 A;  4YPZ A;  5D9F A;  3DCM X;  4YQD A;  1V2X A;  5GMC A;  4YQL A;  4YQ4 A;  4YQ5 A;  1IPA A;  3KW2 A;  2I6D A;  4YQR A;  1NXZ A;  4JAK A;  4X3M A;  1P9P A;  2YY8 A;  2NWA A;  2QMM A;  4YVJ A;  4YQN A;  5GM8 A;  1VHY A;  4YQO A;  1UAM A;  3KY7 A;  4YQS A;  4YQI A;  3BBD A;  2QWV A;  1OY5 A;  3O7B A;  4CNF A;  1MXI A;  4MCD A;  4YVK A;  3QUV A;  4H3Y A;  2V3K A;  4YQ0 A;  4YQ1 A;  4YPX A;  4L69 A;  4YVG A;  3BBH A;  4J3C A;  1J85 A;  2CX8 A;  3ILK A;  4CNE A;  3IC6 A;  4YQ6 A;  2O3A A;  4YQ9 A;  1X7P A;  3AXZ A;  4YQT A;  4CND A; 
#chains in the Genus database with same CATH topology
 5DM7 S;  1K3R A;  5GMB A;  3AII A;  5JVH S;  5GAE W;  1V6Z A;  1D6K A;  1ZJR A;  4YQ2 A;  3L8U A;  1O0B A;  4V19 4;  4KDZ A;  4YQK A;  3NK6 A;  4YQ3 A;  3W2V B;  4U67 S;  3E5Y A;  1UDX A;  5IZN A;  2Z0Y A;  2ZJQ S;  2EGW A;  4E8B A;  1GZ0 A;  4YPY A;  4X3L A;  3PIO S;  1Z85 A;  3PIP S;  4YQB A;  4YQJ A;  2EGV A;  1O6D A;  4JAL A;  4YQC A;  3OIJ A;  4YPW A;  3KTY A;  4YQA A;  4FAK A;  3GYQ A;  3W2W B;  2PNW A;  4JXZ A;  3OII A;  4YQ8 A;  4KGN A;  5HL7 S;  4IO9 S;  4YQG A;  1EUQ A;  3ONP A;  4JXX A;  2HZ7 A;  5BNZ A;  3N4J A;  4MCC A;  4IOC S;  4H4K A;  3N4K A;  5CO4 A;  2HA8 A;  1VHK A;  5GAG W;  4YQ7 A;  2ZJR S;  1X7O A;  2GAE A;  3KNU A;  4XBO A;  4YQP A;  1UAJ A;  5FAI A;  4PZK A;  4FMW A;  4H3Z A;  3CZB A;  3X1L B;  2ZJP S;  3CF5 S;  3BBE A;  3IEF A;  3OIN A;  4YVH A;  4UY8 8;  1VH0 A;  1UAK A;  4MCB A;  1DFU P;  2V3J A;  4JWG A;  4YQQ A;  4RG1 A;  4IG6 A;  1UAL A;  4YVI A;  1NS5 A;  4CNG A;  3NK7 A;  3AIA A;  3AI9 X;  1TO0 A;  4YPZ A;  5D9F A;  3DCM X;  4YQD A;  4WFA S;  1V2X A;  1ZJW A;  5GMC A;  4YQL A;  1QRT A;  4JWH A;  3DLL S;  2G6G A;  4YQ4 A;  4YQ5 A;  1IPA A;  3KW2 A;  4JWJ A;  4P2B A;  2RE8 A;  2I6D A;  4YQR A;  1NXZ A;  2PJJ A;  2AE0 X;  1B75 A;  2RD2 A;  4IOA S;  4JAK A;  1QRS A;  5GAH W;  4X3M A;  1P9P A;  1GTR A;  2YY8 A;  2NWA A;  2QMM A;  4YVJ A;  2PIC A;  4H3S A;  4YQN A;  5GM8 A;  3J7Z V;  1VHY A;  4YQO A;  1UAM A;  1NYL A;  3KY7 A;  4YQS A;  5GAD W;  4YQI A;  3BBD A;  2QWV A;  1OY5 A;  3O7B A;  4JWF A;  5DM6 S;  4CNF A;  1QRU A;  4WF9 S;  1MXI A;  4MCD A;  4YVK A;  3QUV A;  4H3Y A;  4WFN S;  2PI8 A;  4JYZ A;  1GTS A;  5JVG S;  1EUY A;  2V3K A;  1O0C A;  1QTQ A;  1EXD A;  4WCE S;  4YQ0 A;  4YQ1 A;  4YPX A;  4L69 A;  4YVG A;  3BBH A;  4J3C A;  1J85 A;  2CX8 A;  3ILK A;  4CNE A;  3IC6 A;  1FEU A;  4YQ6 A;  2O3A A;  4YQ9 A;  4WFB S;  1X7P A;  3AXZ A;  2G5D A;  4YQT A;  4CND A; 
#chains in the Genus database with same CATH homology
 1K3R A;  5GMB A;  1V6Z A;  1ZJR A;  4YQ2 A;  3L8U A;  4KDZ A;  4YQ3 A;  4YQK A;  3NK6 A;  3E5Y A;  2Z0Y A;  4E8B A;  2EGW A;  1GZ0 A;  4YPY A;  4X3L A;  1Z85 A;  4YQB A;  4YQJ A;  2EGV A;  1O6D A;  4JAL A;  4YQC A;  3OIJ A;  4YPW A;  3KTY A;  4YQA A;  4FAK A;  3GYQ A;  3OII A;  4YQ8 A;  4KGN A;  4YQG A;  3ONP A;  3N4J A;  4MCC A;  3N4K A;  5CO4 A;  2HA8 A;  1VHK A;  4YQ7 A;  1X7O A;  3KNU A;  4XBO A;  4YQP A;  1UAJ A;  5FAI A;  4PZK A;  4FMW A;  4H3Z A;  3BBE A;  3IEF A;  3OIN A;  4YVH A;  1VH0 A;  1UAK A;  4MCB A;  2V3J A;  4JWG A;  4YQQ A;  4RG1 A;  4IG6 A;  1UAL A;  4YVI A;  1NS5 A;  4CNG A;  3NK7 A;  3AIA A;  3AI9 X;  1TO0 A;  4YPZ A;  5D9F A;  3DCM X;  4YQD A;  1V2X A;  5GMC A;  4YQL A;  4JWH A;  4YQ4 A;  4YQ5 A;  1IPA A;  3KW2 A;  4JWJ A;  2I6D A;  4YQR A;  1NXZ A;  4JAK A;  4X3M A;  1P9P A;  2YY8 A;  2NWA A;  2QMM A;  4YVJ A;  4YQN A;  5GM8 A;  1VHY A;  4YQO A;  1UAM A;  3KY7 A;  4YQS A;  4YQI A;  3BBD A;  2QWV A;  1OY5 A;  3O7B A;  4JWF A;  4CNF A;  1MXI A;  4MCD A;  4YVK A;  3QUV A;  4H3Y A;  2V3K A;  4YQ0 A;  4YQ1 A;  4YPX A;  4L69 A;  4YVG A;  3BBH A;  4J3C A;  1J85 A;  2CX8 A;  3ILK A;  4CNE A;  3IC6 A;  4YQ6 A;  2O3A A;  4YQ9 A;  1X7P A;  3AXZ A;  4YQT A;  4CND 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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#similar chains in the pdb database (?% sequence similarity)
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