3OIJA

Crystal structure of saccharomyces cerevisiae nep1/emg1 bound to s-adenosylhomocysteine and 2 molecules of cognate rna
Total Genus 62
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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
62
Knots found
sequence length
225
structure length
211
Chain Sequence
PPVLTSKDKITKRMIVVLAMASLETHKIYVLLNCDDHQGLLDISEARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGILIEVNPTVRIPRTFKRFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHLPTKCRKVTLSFDAPVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYVDEKVGLSNYPLSASVACSKFCHGAEDAWNIL
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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 Essential for mitotic growth 1
publication title Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
pubmed doi rcsb
source organism Saccharomyces cerevisiae
total genus 62
structure length 211
sequence length 225
chains with identical sequence B
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.260: rRNA small subunit pseudouridine methyltransferase Nep1.
pdb deposition date 2010-08-19

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF03587 EMG1 EMG1/NEP1 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 3oijA01
5FAIA 4YQGA 4JALA 3OIIA 1VHKA 3GYQA 4YQCA 4YVJA 2V3KA 4YVKA 4YQ0A 4YQ9A 3BBHA 3NK7A 3BBDA 1V2XA 3ILKA 4RG1A 1X7PA 1UAKA 4YQBA 2QWVA 3KY7A 4YQKA 4YVHA 4XBOA 1IPAA 1X7OA 1Z85A 4YQDA 4YQRA 3L8UA 1K3RA 3KTYA 4YQ7A 3E5YA 4YQ2A 5CO4A 3N4JA 4YQ1A 1P9PA 1VH0A 2V3JA 4YQ8A 3QUVA 3IC6A 1UAMA 2EGWA 3KW2A 4E8BA 4H3YA 4YQSA 3OINA 4X3LA 5GM8A 4YPZA 5GMCA 3AIAA 4IG6A 3O7BA 1NXZA 1TO0A 1V6ZA 4J3CA 4YQ6A 4MCBA 4KGNA 4L69A 3DCMX 2YY8A 4YQTA 4KDZA 4YQJA 4MCDA 3ONPA 4YQLA 3KNUA 4FAKA 4YQIA 4YQQA 4YPWA 1UAJA 4MCCA 4JAKA 2EGVA 4PZKA 4YVGA 4YVIA 4YQNA 4YQOA 3BBEA 4YQ5A 1VHYA 5D9FA 1MXIA 4YQAA 1NS5A 3NK6A 4CNGA 5GMBA 2Z0YA 4YQ3A 4YQ4A 1UALA 2QMMA 1O6DA 3AXZA 4YPYA 1OY5A 4YQPA 1GZ0A 4CNFA 4X3MA 3IEFA 4YPXA 3N4KA 4CNEA 2HA8A 1J85A 2CX8A 1ZJRA 2O3AA 4CNDA 3OIJA 4H3ZA 3AI9X 2I6DA
chains in the Genus database with same CATH superfamily
5FAIA 4YQGA 4JALA 3OIIA 1VHKA 3GYQA 4YQCA 4YVJA 2V3KA 4YVKA 4YQ0A 4YQ9A 3BBHA 3NK7A 3BBDA 1V2XA 3ILKA 4RG1A 1X7PA 1UAKA 4YQBA 2QWVA 3KY7A 4YQKA 4YVHA 4XBOA 1IPAA 1X7OA 1Z85A 4YQDA 4YQRA 3L8UA 1K3RA 3KTYA 4YQ7A 3E5YA 4YQ2A 5CO4A 3N4JA 4YQ1A 1P9PA 1VH0A 2V3JA 4YQ8A 3QUVA 3IC6A 1UAMA 2EGWA 3KW2A 4JWJA 4E8BA 4H3YA 4YQSA 3OINA 4X3LA 5GM8A 4YPZA 5GMCA 3AIAA 4IG6A 3O7BA 1NXZA 1TO0A 1V6ZA 4J3CA 4YQ6A 4MCBA 4KGNA 4L69A 3DCMX 2YY8A 4YQTA 4JWGA 4JWHA 4KDZA 4YQJA 4MCDA 3ONPA 4YQLA 3KNUA 4FAKA 4YQIA 4YQQA 4YPWA 1UAJA 4MCCA 4JAKA 2EGVA 4PZKA 4YVGA 4YVIA 4FMWA 4YQNA 4YQOA 3BBEA 4YQ5A 1VHYA 5D9FA 1MXIA 4YQAA 1NS5A 3NK6A 4CNGA 5GMBA 2Z0YA 4YQ3A 4YQ4A 1UALA 2QMMA 1O6DA 4JWFA 3AXZA 4YPYA 1OY5A 4YQPA 1GZ0A 4CNFA 4X3MA 3IEFA 4YPXA 3N4KA 4CNEA 2HA8A 1J85A 2CX8A 1ZJRA 2O3AA 4CNDA 3OIJA 4H3ZA 3AI9X 2I6DA
chains in the Genus database with same CATH topology
5FAIA 4YQGA 4JALA 3OIIA 1VHKA 3GYQA 4YQCA 4YVJA 2V3KA 4YVKA 4YQ0A 4YQ9A 3BBHA 3NK7A 3BBDA 1V2XA 3ILKA 4RG1A 1X7PA 1UAKA 4YQBA 2QWVA 3KY7A 4YQKA 4YVHA 4XBOA 1IPAA 1X7OA 1Z85A 4YQDA 4YQRA 3L8UA 1K3RA 3KTYA 4YQ7A 3E5YA 4YQ2A 5CO4A 3N4JA 4YQ1A 1P9PA 1VH0A 2V3JA 4YQ8A 3QUVA 3IC6A 1UAMA 2EGWA 3KW2A 4JWJA 4E8BA 4H3YA 4YQSA 3OINA 4X3LA 5GM8A 4YPZA 5GMCA 3AIAA 4IG6A 3O7BA 1NXZA 1TO0A 1V6ZA 4J3CA 4YQ6A 4MCBA 4KGNA 4L69A 3DCMX 2YY8A 4YQTA 4JWGA 4JWHA 4KDZA 4YQJA 4MCDA 3ONPA 4YQLA 3KNUA 4FAKA 4YQIA 4YQQA 4YPWA 1UAJA 4MCCA 4JAKA 2EGVA 4PZKA 4YVGA 4YVIA 4FMWA 4YQNA 4YQOA 3BBEA 4YQ5A 1VHYA 5D9FA 1MXIA 4YQAA 1NS5A 3NK6A 4CNGA 5GMBA 2Z0YA 4YQ3A 4YQ4A 1UALA 2QMMA 1O6DA 4JWFA 3AXZA 4YPYA 1OY5A 4YQPA 1GZ0A 4CNFA 4X3MA 3IEFA 4YPXA 3N4KA 4CNEA 2HA8A 1J85A 2CX8A 1ZJRA 2O3AA 4CNDA 3OIJA 4H3ZA 3AI9X 2I6DA
chains in the Genus database with same CATH homology


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