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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publication title Crystal structure of probable rRNA-methyltransferase from Porphyromonas gingivalis
rcsb
source organism Porphyromonas gingivalis atcc 33277
molecule tags Transferase
molecule keywords Probable r-RNA methyltransferase
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
2EGWA 4YPXA 4YQ5A 4YQGA 3DCMX 4XBOA 3N4KA 3N4JA 1OY5A 4X3LA 4YQOA 1UAJA 4CNGA 4YQLA 1O6DA 4PZKA 2CX8A 4FAKA 4YQJA 4YQ6A 1K3RA 4YQSA 4E8BA 4H3ZA 4L69A 3KTYA 4IG6A 3BBHA 1VHKA 4YQ9A 4YVJA 4YQIA 3NK7A 2YY8A 4YQ3A 4YQAA 3GYQA 4YPZA 4MCCA 4YQ2A 2V3JA 3KY7A 3QUVA 1VH0A 4CNEA 4YQPA 2QMMA 4RG1A 4KGNA 4YQ0A 4YQ8A 4YQ1A 2I6DA 1UAMA 3NK6A 3AXZA 4YQ4A 3KW2A 4YVKA 3BBDA 4H3YA 4CNDA 1TO0A 3AI9X 1J85A 1ZJRA 4KDZA 5GM8A 1X7OA 2Z0YA 4YVIA 4YQRA 3OIJA 3IEFA 2QWVA 4YVHA 3E5YA 3L8UA 4YQNA 1GZ0A 1NXZA 3O7BA 1NS5A 1V6ZA 2EGVA 1UAKA 1Z85A 4JAKA 4MCBA 3KNUA 4X3MA 4JALA 4YQQA 2NWAA 3AIAA 1IPAA 1X7PA 1UALA 3BBEA 5GMCA 2O3AA 1MXIA 4YPWA 1V2XA 5GMBA 4YVGA 4CNFA 2HA8A 4MCDA 1VHYA 1P9PA 5D9FA 4YQTA 4YQBA 2V3KA 4YPYA 3IC6A 4YQDA 3OINA 4YQ7A 3OIIA 5CO4A 3ONPA 5FAIA 4YQKA 4J3CA 4YQCA 3ILKA
chains in the Genus database with same CATH superfamily
2EGWA 4YPXA 4YQ5A 4YQGA 3DCMX 4XBOA 1GTSA 3N4KA 4U67S 1OY5A 3N4JA 4X3LA 4YQOA 1UAJA 1B75A 4CNGA 1QRTA 4YQLA 3CZBA 1QRSA 1O6DA 1FEUA 4PZKA 2CX8A 3J7ZV 4FAKA 4YQJA 1EUQA 4FMWA 4YQ6A 2HZ7A 5GAGW 4IO9S 1K3RA 4YQSA 4IOCS 5HL7S 4E8BA 4H3ZA 1UDXA 4L69A 3KTYA 4IG6A 5BNZA 3PIPS 5GAHW 3BBHA 1VHKA 4YQ9A 4YVJA 4YQIA 1DFUP 2YY8A 3NK7A 4YQ3A 4YQAA 3GYQA 4YPZA 2G5DA 4JYZA 4MCCA 5GAEW 4H3SA 4YQ2A 2V3JA 3KY7A 3QUVA 5GADW 1VH0A 4CNEA 3X1LB 2QMMA 4YQPA 4RG1A 4KGNA 4YQ0A 2RD2A 5JVGS 4YQ8A 4YQ1A 2I6DA 1UAMA 4WFBS 4V194 3NK6A 3AXZA 4YQ4A 3KW2A 4YVKA 3BBDA 4H3YA 4CNDA 4JXXA 3W2WB 1TO0A 3AI9X 1J85A 1ZJRA 4KDZA 4IOAS 5GM8A 1X7OA 1EXDA 2Z0YA 4WF9S 4YQRA 4YVIA 1EUYA 4JWGA 3OIJA 3IEFA 2QWVA 2ZJQS 4JWFA 4JWJA 4YVHA 1QTQA 4WFNS 2RE8A 3E5YA 2ZJPS 3L8UA 4YQNA 4JXZA 1GZ0A 1NXZA 3O7BA 1NS5A 4P2BA 1V6ZA 2EGVA 4H4KA 1Z85A 1O0BA 1O0CA 1UAKA 4JAKA 4MCBA 4WCES 3KNUA 4X3MA 4JALA 4YQQA 2PJJA 4WFAS 1D6KA 3W2VB 4JWHA 5DM7S 2NWAA 3AIAA 3PIOS 1IPAA 1X7PA 2PICA 1UALA 3BBEA 5GMCA 2PNWA 2O3AA 1MXIA 4YPWA 1ZJWA 1V2XA 5GMBA 4YVGA 5JVHS 4CNFA 2HA8A 2GAEA 4MCDA 1VHYA 1NYLA 1P9PA 5D9FA 4YQTA 3CF5S 2V3KA 4YPYA 4YQBA 5IZNA 3IC6A 5DM6S 4UY88 4YQDA 3OINA 2PI8A 2AE0X 4YQ7A 3OIIA 3AIIA 3ONPA 2G6GA 5CO4A 5FAIA 2ZJRS 4YQKA 4J3CA 4YQCA 1QRUA 3DLLS 1GTRA 3ILKA
chains in the Genus database with same CATH topology
2EGWA 4YPXA 4YQ5A 4YQGA 3DCMX 4XBOA 3N4KA 3N4JA 1OY5A 4X3LA 4YQOA 1UAJA 4CNGA 4YQLA 1O6DA 4PZKA 2CX8A 4FAKA 4YQJA 4FMWA 4YQ6A 1K3RA 4YQSA 4E8BA 4H3ZA 4L69A 3KTYA 4IG6A 3BBHA 1VHKA 4YQ9A 4YVJA 4YQIA 3NK7A 2YY8A 4YQ3A 4YQAA 3GYQA 4YPZA 4MCCA 4YQ2A 2V3JA 3KY7A 3QUVA 1VH0A 4CNEA 4YQPA 2QMMA 4RG1A 4KGNA 4YQ0A 4YQ8A 4YQ1A 2I6DA 1UAMA 3NK6A 3AXZA 4YQ4A 3KW2A 4YVKA 3BBDA 4H3YA 4CNDA 1TO0A 3AI9X 1J85A 1ZJRA 4KDZA 5GM8A 1X7OA 2Z0YA 4YVIA 4YQRA 4JWGA 3OIJA 3IEFA 2QWVA 4JWFA 4YVHA 4JWJA 3E5YA 3L8UA 4YQNA 1GZ0A 1NXZA 3O7BA 1NS5A 1V6ZA 2EGVA 1UAKA 1Z85A 4JAKA 4MCBA 3KNUA 4X3MA 4JALA 4YQQA 4JWHA 2NWAA 3AIAA 1IPAA 1X7PA 1UALA 3BBEA 5GMCA 2O3AA 1MXIA 4YPWA 1V2XA 5GMBA 4YVGA 4CNFA 2HA8A 4MCDA 1VHYA 1P9PA 5D9FA 4YQTA 4YQBA 2V3KA 4YPYA 3IC6A 4YQDA 3OINA 4YQ7A 3OIIA 5CO4A 3ONPA 5FAIA 4YQKA 4J3CA 4YQCA 3ILKA
chains in the Genus database with same CATH homology


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