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


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