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


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