4FAKA

Crystal structure of orfx in complex with s-adenosylmethionine
Total Genus 53
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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
53
Knots found
sequence length
163
structure length
163
Chain Sequence
b'AAEFMKITILAVGKLKEKYWKQAIAEYEKRLGPYTKIDIIEVPDEKAPENMSDKEIEQVKEKEGQRILAKIKPQSTVITLEIQGKMLSSEGLAQELNQRMTQGQSDFVFVIGGSNGLHKDVLQRSNYALSFSKMTFPHQMMRVVLIEQVYRAFKIMRGEAYHK'
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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 Ribosomal RNA large subunit methyltransferase H
publication title Characterization of the Staphylococcus aureus rRNA Methyltransferase Encoded by orfX, the Gene Containing the Staphylococcal Chromosome Cassette mec (SCCmec) Insertion Site.
pubmed doi rcsb
source organism Staphylococcus aureus
molecule tags Transferase, ribosomal protein
total genus 53
structure length 163
sequence length 163
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.177: 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase.
pdb deposition date 2012-05-22

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF02590 SPOUT_MTase Predicted SPOUT methyltransferase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 4fakA00
1VHKA 3KW2A 4YQ4A 4JAKA 5GMCA 2QWVA 4E8BA 3AIAA 3ONPA 2YY8A 1ZJRA 3E5YA 1UAKA 1NS5A 4YVGA 1O6DA 4YQ6A 4CNGA 3AXZA 3OIIA 4YQKA 4YPWA 3IC6A 3BBDA 2Z0YA 1TO0A 2V3JA 4KDZA 1OY5A 4YQQA 4YVJA 4L69A 1X7PA 2HA8A 4CNEA 2EGVA 4YQ2A 1IPAA 1P9PA 4YQIA 1J85A 4YQOA 1V6ZA 3NK6A 3KTYA 4PZKA 3KY7A 4YQGA 5GM8A 4X3MA 1K3RA 4H3YA 4FAKA 5D9FA 3IEFA 2I6DA 4YQSA 2QMMA 3L8UA 4YVKA 4MCCA 4YQ5A 4X3LA 1UAJA 4YQ3A 4IG6A 4JALA 2O3AA 4CNFA 3BBHA 1V2XA 4YPXA 5GMBA 2V3KA 4H3ZA 4YVHA 3N4KA 4YQ8A 4RG1A 4YQ1A 4YQCA 3BBEA 4YQDA 3ILKA 3OIJA 3OINA 2CX8A 3QUVA 4YQBA 3DCMX 4XBOA 4YQ7A 1Z85A 3GYQA 4YQAA 4YQJA 1X7OA 5FAIA 1NXZA 3KNUA 4YVIA 3N4JA 4CNDA 4YPYA 4YQ0A 1GZ0A 1MXIA 4KGNA 1VHYA 3NK7A 4YQLA 4YQ9A 4YPZA 4MCBA 4YQPA 5CO4A 4J3CA 4YQTA 3AI9X 1VH0A 3O7BA 4MCDA 1UALA 1UAMA 4YQRA 4YQNA 2EGWA
chains in the Genus database with same CATH superfamily
1VHKA 3KW2A 4YQ4A 4JAKA 5GMCA 2QWVA 4E8BA 3AIAA 3ONPA 2YY8A 1ZJRA 3E5YA 1UAKA 1NS5A 4YVGA 4JWFA 1O6DA 4YQ6A 4CNGA 4FMWA 3AXZA 3OIIA 4YQKA 4YPWA 3IC6A 3BBDA 2Z0YA 1TO0A 2V3JA 4KDZA 1OY5A 4YQQA 4YVJA 4L69A 1X7PA 2HA8A 4CNEA 2EGVA 4YQ2A 1IPAA 1P9PA 4YQIA 1J85A 4YQOA 1V6ZA 3NK6A 3KTYA 4PZKA 3KY7A 4YQGA 5GM8A 4X3MA 1K3RA 4H3YA 4FAKA 5D9FA 3IEFA 2I6DA 4YQSA 2QMMA 3L8UA 4JWGA 4YVKA 4MCCA 4YQ5A 4X3LA 1UAJA 4YQ3A 4IG6A 4JALA 2O3AA 4CNFA 3BBHA 1V2XA 4YPXA 5GMBA 2V3KA 4H3ZA 4YVHA 3N4KA 4YQ8A 4RG1A 4YQ1A 4YQCA 3BBEA 4YQDA 3ILKA 3OIJA 3OINA 2CX8A 3QUVA 4YQBA 3DCMX 4XBOA 4YQ7A 1Z85A 3GYQA 4YQAA 4YQJA 1X7OA 5FAIA 1NXZA 3KNUA 4YVIA 3N4JA 4CNDA 4YPYA 4YQ0A 1GZ0A 1MXIA 4KGNA 1VHYA 3NK7A 4YQLA 4YQ9A 4YPZA 4MCBA 4YQPA 5CO4A 4J3CA 4YQTA 4JWJA 3AI9X 1VH0A 4JWHA 3O7BA 4MCDA 1UALA 1UAMA 4YQRA 4YQNA 2EGWA
chains in the Genus database with same CATH topology
1VHKA 3KW2A 4YQ4A 4JAKA 5GMCA 2QWVA 4E8BA 3AIAA 3ONPA 2YY8A 1ZJRA 3E5YA 1UAKA 1NS5A 4YVGA 4JWFA 1O6DA 4YQ6A 4CNGA 4FMWA 3AXZA 3OIIA 4YQKA 4YPWA 3IC6A 3BBDA 2Z0YA 1TO0A 2V3JA 4KDZA 1OY5A 4YQQA 4YVJA 4L69A 1X7PA 2HA8A 4CNEA 2EGVA 4YQ2A 1IPAA 1P9PA 4YQIA 1J85A 4YQOA 1V6ZA 3NK6A 3KTYA 4PZKA 3KY7A 4YQGA 5GM8A 4X3MA 1K3RA 4H3YA 4FAKA 5D9FA 3IEFA 2I6DA 4YQSA 2QMMA 3L8UA 4JWGA 4YVKA 4MCCA 4YQ5A 4X3LA 1UAJA 4YQ3A 4IG6A 4JALA 2O3AA 4CNFA 3BBHA 1V2XA 4YPXA 5GMBA 2V3KA 4H3ZA 4YVHA 3N4KA 4YQ8A 4RG1A 4YQ1A 4YQCA 3BBEA 4YQDA 3ILKA 3OIJA 3OINA 2CX8A 3QUVA 4YQBA 3DCMX 4XBOA 4YQ7A 1Z85A 3GYQA 4YQAA 4YQJA 1X7OA 5FAIA 1NXZA 3KNUA 4YVIA 3N4JA 4CNDA 4YPYA 4YQ0A 1GZ0A 1MXIA 4KGNA 1VHYA 3NK7A 4YQLA 4YQ9A 4YPZA 4MCBA 4YQPA 5CO4A 4J3CA 4YQTA 4JWJA 3AI9X 1VH0A 4JWHA 3O7BA 4MCDA 1UALA 1UAMA 4YQRA 4YQNA 2EGWA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1VHK A;  3KW2 A;  4YQ4 A;  4JAK A;  5GMC A;  2QWV A;  4E8B A;  3AIA A;  3ONP A;  2YY8 A;  1ZJR A;  3E5Y A;  1UAK A;  1NS5 A;  4YVG A;  1O6D A;  4YQ6 A;  4CNG A;  3AXZ A;  3OII A;  4YQK A;  4YPW A;  3IC6 A;  3BBD A;  2Z0Y A;  1TO0 A;  2V3J A;  4KDZ A;  1OY5 A;  4YQQ A;  4YVJ A;  4L69 A;  1X7P A;  2HA8 A;  4CNE A;  2EGV A;  4YQ2 A;  1IPA A;  1P9P A;  4YQI A;  1J85 A;  4YQO A;  1V6Z A;  3NK6 A;  3KTY A;  4PZK A;  3KY7 A;  4YQG A;  5GM8 A;  4X3M A;  1K3R A;  4H3Y A;  4FAK A;  5D9F A;  3IEF A;  2I6D A;  4YQS A;  2QMM A;  3L8U A;  4YVK A;  4MCC A;  4YQ5 A;  4X3L A;  1UAJ A;  4YQ3 A;  4IG6 A;  4JAL A;  2O3A A;  4CNF A;  3BBH A;  1V2X A;  4YPX A;  5GMB A;  2V3K A;  4H3Z A;  4YVH A;  3N4K A;  4YQ8 A;  4RG1 A;  4YQ1 A;  4YQC A;  3BBE A;  4YQD A;  3ILK A;  3OIJ A;  3OIN A;  2CX8 A;  3QUV A;  4YQB A;  3DCM X;  4XBO A;  4YQ7 A;  1Z85 A;  3GYQ A;  4YQA A;  4YQJ A;  1X7O A;  5FAI A;  1NXZ A;  3KNU A;  4YVI A;  3N4J A;  4CND A;  4YPY A;  4YQ0 A;  1GZ0 A;  1MXI A;  4KGN A;  1VHY A;  3NK7 A;  4YQL A;  4YQ9 A;  4YPZ A;  4MCB A;  4YQP A;  5CO4 A;  4J3C A;  4YQT A;  3AI9 X;  1VH0 A;  3O7B A;  4MCD A;  1UAL A;  1UAM A;  4YQR A;  4YQN A;  2EGW A; 
#chains in the Genus database with same CATH topology
 1VHK A;  3KW2 A;  4YQ4 A;  4JAK A;  5GMC A;  2QWV A;  4E8B A;  3AIA A;  3ONP A;  2YY8 A;  1ZJR A;  3E5Y A;  1UAK A;  1NS5 A;  4YVG A;  4JWF A;  1O6D A;  4YQ6 A;  4CNG A;  4FMW A;  3AXZ A;  3OII A;  4YQK A;  4YPW A;  3IC6 A;  3BBD A;  2Z0Y A;  1TO0 A;  2V3J A;  4KDZ A;  1OY5 A;  4YQQ A;  4YVJ A;  4L69 A;  1X7P A;  2HA8 A;  4CNE A;  2EGV A;  4YQ2 A;  1IPA A;  1P9P A;  4YQI A;  1J85 A;  4YQO A;  1V6Z A;  3NK6 A;  3KTY A;  4PZK A;  3KY7 A;  4YQG A;  5GM8 A;  4X3M A;  1K3R A;  4H3Y A;  4FAK A;  5D9F A;  3IEF A;  2I6D A;  4YQS A;  2QMM A;  3L8U A;  4JWG A;  4YVK A;  4MCC A;  4YQ5 A;  4X3L A;  1UAJ A;  4YQ3 A;  4IG6 A;  4JAL A;  2O3A A;  4CNF A;  3BBH A;  1V2X A;  4YPX A;  5GMB A;  2V3K A;  4H3Z A;  4YVH A;  3N4K A;  4YQ8 A;  4RG1 A;  4YQ1 A;  4YQC A;  3BBE A;  4YQD A;  3ILK A;  3OIJ A;  3OIN A;  2CX8 A;  3QUV A;  4YQB A;  3DCM X;  4XBO A;  4YQ7 A;  1Z85 A;  3GYQ A;  4YQA A;  4YQJ A;  1X7O A;  5FAI A;  1NXZ A;  3KNU A;  4YVI A;  3N4J A;  4CND A;  4YPY A;  4YQ0 A;  1GZ0 A;  1MXI A;  4KGN A;  1VHY A;  3NK7 A;  4YQL A;  4YQ9 A;  4YPZ A;  4MCB A;  4YQP A;  5CO4 A;  4J3C A;  4YQT A;  4JWJ A;  3AI9 X;  1VH0 A;  4JWH A;  3O7B A;  4MCD A;  1UAL A;  1UAM A;  4YQR A;  4YQN A;  2EGW A; 
#chains in the Genus database with same CATH homology
 1VHK A;  3KW2 A;  4YQ4 A;  4JAK A;  5GMC A;  2QWV A;  4E8B A;  3AIA A;  3ONP A;  2YY8 A;  1ZJR A;  3E5Y A;  1UAK A;  1NS5 A;  4YVG A;  4JWF A;  1O6D A;  4YQ6 A;  4CNG A;  4FMW A;  3AXZ A;  3OII A;  4YQK A;  4YPW A;  3IC6 A;  3BBD A;  2Z0Y A;  1TO0 A;  2V3J A;  4KDZ A;  1OY5 A;  4YQQ A;  4YVJ A;  4L69 A;  1X7P A;  2HA8 A;  4CNE A;  2EGV A;  4YQ2 A;  1IPA A;  1P9P A;  4YQI A;  1J85 A;  4YQO A;  1V6Z A;  3NK6 A;  3KTY A;  4PZK A;  3KY7 A;  4YQG A;  5GM8 A;  4X3M A;  1K3R A;  4H3Y A;  4FAK A;  5D9F A;  3IEF A;  2I6D A;  4YQS A;  2QMM A;  3L8U A;  4JWG A;  4YVK A;  4MCC A;  4YQ5 A;  4X3L A;  1UAJ A;  4YQ3 A;  4IG6 A;  4JAL A;  2O3A A;  4CNF A;  3BBH A;  1V2X A;  4YPX A;  5GMB A;  2V3K A;  4H3Z A;  4YVH A;  3N4K A;  4YQ8 A;  4RG1 A;  4YQ1 A;  4YQC A;  3BBE A;  4YQD A;  3ILK A;  3OIJ A;  3OIN A;  2CX8 A;  3QUV A;  4YQB A;  3DCM X;  4XBO A;  4YQ7 A;  1Z85 A;  3GYQ A;  4YQA A;  4YQJ A;  1X7O A;  5FAI A;  1NXZ A;  3KNU A;  4YVI A;  3N4J A;  4CND A;  4YPY A;  4YQ0 A;  1GZ0 A;  1MXI A;  4KGN A;  1VHY A;  3NK7 A;  4YQL A;  4YQ9 A;  4YPZ A;  4MCB A;  4YQP A;  5CO4 A;  4J3C A;  4YQT A;  4JWJ A;  3AI9 X;  1VH0 A;  4JWH A;  3O7B A;  4MCD A;  1UAL A;  1UAM A;  4YQR A;  4YQN A;  2EGW 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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