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


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