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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publication title Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
pubmed doi rcsb
molecule tags Ribosomal protein
source organism Saccharomyces cerevisiae
molecule keywords Essential for mitotic growth 1
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
3KW2A 3IEFA 4CNGA 1V6ZA 4JAKA 4YQIA 4JALA 3OINA 4YQJA 1Z85A 4J3CA 1MXIA 4XBOA 4YQ1A 1VHKA 4PZKA 2QWVA 1NXZA 3N4JA 3NK7A 3NK6A 5GM8A 2O3AA 4YQPA 2YY8A 3AXZA 4YPXA 4YVJA 4H3ZA 1J85A 3OIIA 4MCBA 4YQDA 3KNUA 2Z0YA 1V2XA 2HA8A 5GMBA 1NS5A 4YPZA 3AI9X 1IPAA 1OY5A 4YQ9A 5CO4A 1K3RA 4YQ6A 4YVKA 4KDZA 4YPWA 4CNEA 1X7OA 3BBHA 4YQLA 4YQGA 4YQ4A 1ZJRA 2EGVA 3L8UA 1UAMA 4YVHA 4YQOA 1UALA 4YQTA 4H3YA 4IG6A 4RG1A 3IC6A 2V3JA 3QUVA 1GZ0A 1TO0A 4FAKA 4YQ5A 3DCMX 2QMMA 4KGNA 4YQ3A 3O7BA 3E5YA 3KTYA 5FAIA 4YQNA 2I6DA 4MCDA 4YQ2A 4L69A 4CNDA 4YQSA 1UAJA 4YQ8A 2V3KA 4YQ0A 4YVIA 3GYQA 4YQAA 1VH0A 3ONPA 1X7PA 4X3LA 4YPYA 4MCCA 5D9FA 3BBDA 5GMCA 3BBEA 1UAKA 4YQRA 4X3MA 3ILKA 4YQQA 4CNFA 4YQ7A 3OIJA 3AIAA 1VHYA 3N4KA 2CX8A 4YQKA 4E8BA 4YVGA 1P9PA 2EGWA 1O6DA 4YQCA 3KY7A 4YQBA
chains in the Genus database with same CATH superfamily
3KW2A 3IEFA 4CNGA 1V6ZA 4JAKA 4YQIA 4JWFA 4JALA 3OINA 4YQJA 1Z85A 4J3CA 1MXIA 4XBOA 4YQ1A 1VHKA 4PZKA 2QWVA 1NXZA 3N4JA 3NK7A 3NK6A 5GM8A 2O3AA 4YQPA 2YY8A 3AXZA 4YPXA 4YVJA 4H3ZA 1J85A 3OIIA 4MCBA 4YQDA 3KNUA 2Z0YA 1V2XA 2HA8A 5GMBA 1NS5A 4YPZA 3AI9X 1IPAA 1OY5A 4YQ9A 5CO4A 1K3RA 4YQ6A 4YVKA 4KDZA 4YPWA 4CNEA 1X7OA 3BBHA 4YQLA 4YQGA 4YQ4A 1ZJRA 2EGVA 3L8UA 4FMWA 1UAMA 4YVHA 4YQOA 1UALA 4YQTA 4H3YA 4IG6A 4RG1A 3IC6A 2V3JA 3QUVA 1GZ0A 1TO0A 4FAKA 4YQ5A 3DCMX 4JWJA 2QMMA 4KGNA 4YQ3A 3O7BA 3E5YA 3KTYA 5FAIA 4YQNA 2I6DA 4MCDA 4YQ2A 4L69A 4CNDA 4YQSA 1UAJA 4YQ8A 2V3KA 4YQ0A 4YVIA 3GYQA 4YQAA 1VH0A 3ONPA 1X7PA 4X3LA 4JWGA 4YPYA 4MCCA 5D9FA 3BBDA 5GMCA 3BBEA 1UAKA 4YQRA 4X3MA 3ILKA 4YQQA 4CNFA 4YQ7A 3OIJA 3AIAA 1VHYA 3N4KA 2CX8A 4YQKA 4E8BA 4YVGA 1P9PA 2EGWA 4JWHA 1O6DA 4YQCA 3KY7A 4YQBA
chains in the Genus database with same CATH topology
3KW2A 3IEFA 4CNGA 1V6ZA 4JAKA 4YQIA 4JWFA 4JALA 3OINA 4YQJA 1Z85A 4J3CA 1MXIA 4XBOA 4YQ1A 1VHKA 4PZKA 2QWVA 1NXZA 3N4JA 3NK7A 3NK6A 5GM8A 2O3AA 4YQPA 2YY8A 3AXZA 4YPXA 4YVJA 4H3ZA 1J85A 3OIIA 4MCBA 4YQDA 3KNUA 2Z0YA 1V2XA 2HA8A 5GMBA 1NS5A 4YPZA 3AI9X 1IPAA 1OY5A 4YQ9A 5CO4A 1K3RA 4YQ6A 4YVKA 4KDZA 4YPWA 4CNEA 1X7OA 3BBHA 4YQLA 4YQGA 4YQ4A 1ZJRA 2EGVA 3L8UA 4FMWA 1UAMA 4YVHA 4YQOA 1UALA 4YQTA 4H3YA 4IG6A 4RG1A 3IC6A 2V3JA 3QUVA 1GZ0A 1TO0A 4FAKA 4YQ5A 3DCMX 4JWJA 2QMMA 4KGNA 4YQ3A 3O7BA 3E5YA 3KTYA 5FAIA 4YQNA 2I6DA 4MCDA 4YQ2A 4L69A 4CNDA 4YQSA 1UAJA 4YQ8A 2V3KA 4YQ0A 4YVIA 3GYQA 4YQAA 1VH0A 3ONPA 1X7PA 4X3LA 4JWGA 4YPYA 4MCCA 5D9FA 3BBDA 5GMCA 3BBEA 1UAKA 4YQRA 4X3MA 3ILKA 4YQQA 4CNFA 4YQ7A 3OIJA 3AIAA 1VHYA 3N4KA 2CX8A 4YQKA 4E8BA 4YVGA 1P9PA 2EGWA 4JWHA 1O6DA 4YQCA 3KY7A 4YQBA
chains in the Genus database with same CATH homology


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