3OIIA

Crystal structure of saccharomyces cerevisiae nep1/emg1 bound to s-adenosylhomocysteine
Total Genus 67
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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
67
Knots found
sequence length
225
structure length
216
Chain Sequence
PPVLTSKDKITKRMIVVLAMASLETHKIYVLLNCDDHQGLLKKMGRDISEARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGILIEVNPTVRIPRTFKRFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHLPTKCRKVTLSFDAPVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYVDEKVGLSNYPLSASVACSKFCHGAEDAWNIL
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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 67
structure length 216
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 3oiiA01
3AI9X 2Z0YA 1V6ZA 4YQ4A 3KY7A 4YPZA 4YQGA 3GYQA 2O3AA 4YQJA 5GMBA 4YQ2A 4YPXA 3AIAA 3OIIA 4YQTA 3BBEA 4YQIA 4IG6A 4RG1A 4MCCA 1NS5A 4YQNA 2V3KA 3BBHA 4YVJA 3KTYA 1UAKA 4E8BA 4YQ0A 4KGNA 3IC6A 3ONPA 1V2XA 4JALA 4YVHA 4YQQA 4CNGA 3O7BA 1MXIA 1X7PA 4YQ3A 3ILKA 4YQLA 2I6DA 4YPYA 3DCMX 4YQBA 1UAJA 2CX8A 4CNEA 3N4JA 1VHKA 3IEFA 4YVGA 4KDZA 4YQ7A 3NK7A 3OIJA 4YQ5A 1K3RA 4YQRA 4YQDA 1UALA 5GM8A 4MCBA 3KNUA 2YY8A 1GZ0A 4YQCA 2QMMA 3OINA 3KW2A 1X7OA 4PZKA 5GMCA 4JAKA 4YQSA 4YQ9A 1J85A 2QWVA 4YQ1A 5FAIA 2EGWA 1VHYA 1TO0A 4X3MA 2EGVA 4H3ZA 3BBDA 4YPWA 4YQOA 1O6DA 4YQ6A 1VH0A 2HA8A 3N4KA 1NXZA 3AXZA 4MCDA 1UAMA 5CO4A 4YQAA 3NK6A 1IPAA 4YVIA 4L69A 4H3YA 3L8UA 4J3CA 4YQ8A 4CNDA 3E5YA 4FAKA 5D9FA 4YQKA 2V3JA 4YQPA 1OY5A 4XBOA 3QUVA 4CNFA 1ZJRA 4YVKA 4X3LA 1Z85A 1P9PA
chains in the Genus database with same CATH superfamily
3AI9X 2Z0YA 1V6ZA 4YQ4A 3KY7A 4YPZA 4YQGA 3GYQA 2O3AA 4YQJA 5GMBA 4YQ2A 4YPXA 3AIAA 3OIIA 4YQTA 3BBEA 4YQIA 4IG6A 4RG1A 4JWHA 4MCCA 1NS5A 4YQNA 2V3KA 3BBHA 4YVJA 3KTYA 1UAKA 4E8BA 4YQ0A 4KGNA 3IC6A 3ONPA 1V2XA 4JALA 4YVHA 4FMWA 4YQQA 4CNGA 3O7BA 1MXIA 4JWGA 1X7PA 4YQ3A 4JWFA 3ILKA 4YQLA 2I6DA 4YPYA 3DCMX 4YQBA 1UAJA 2CX8A 4CNEA 3N4JA 1VHKA 3IEFA 4YVGA 4KDZA 4YQ7A 3NK7A 3OIJA 4YQ5A 1K3RA 4JWJA 4YQRA 4YQDA 1UALA 5GM8A 4MCBA 3KNUA 2YY8A 1GZ0A 4YQCA 2QMMA 3OINA 3KW2A 1X7OA 4PZKA 5GMCA 4JAKA 4YQSA 4YQ9A 1J85A 2QWVA 4YQ1A 5FAIA 2EGWA 1VHYA 1TO0A 4X3MA 2EGVA 4H3ZA 3BBDA 4YPWA 4YQOA 1O6DA 4YQ6A 1VH0A 2HA8A 3N4KA 1NXZA 3AXZA 4MCDA 1UAMA 5CO4A 4YQAA 3NK6A 1IPAA 4YVIA 4L69A 4H3YA 3L8UA 4J3CA 4YQ8A 4CNDA 3E5YA 4FAKA 5D9FA 4YQKA 2V3JA 4YQPA 1OY5A 4XBOA 3QUVA 4CNFA 1ZJRA 4YVKA 4X3LA 1Z85A 1P9PA
chains in the Genus database with same CATH topology
3AI9X 2Z0YA 1V6ZA 4YQ4A 3KY7A 4YPZA 4YQGA 3GYQA 2O3AA 4YQJA 5GMBA 4YQ2A 4YPXA 3AIAA 3OIIA 4YQTA 3BBEA 4YQIA 4IG6A 4RG1A 4JWHA 4MCCA 1NS5A 4YQNA 2V3KA 3BBHA 4YVJA 3KTYA 1UAKA 4E8BA 4YQ0A 4KGNA 3IC6A 3ONPA 1V2XA 4JALA 4YVHA 4FMWA 4YQQA 4CNGA 3O7BA 1MXIA 4JWGA 1X7PA 4YQ3A 4JWFA 3ILKA 4YQLA 2I6DA 4YPYA 3DCMX 4YQBA 1UAJA 2CX8A 4CNEA 3N4JA 1VHKA 3IEFA 4YVGA 4KDZA 4YQ7A 3NK7A 3OIJA 4YQ5A 1K3RA 4JWJA 4YQRA 4YQDA 1UALA 5GM8A 4MCBA 3KNUA 2YY8A 1GZ0A 4YQCA 2QMMA 3OINA 3KW2A 1X7OA 4PZKA 5GMCA 4JAKA 4YQSA 4YQ9A 1J85A 2QWVA 4YQ1A 5FAIA 2EGWA 1VHYA 1TO0A 4X3MA 2EGVA 4H3ZA 3BBDA 4YPWA 4YQOA 1O6DA 4YQ6A 1VH0A 2HA8A 3N4KA 1NXZA 3AXZA 4MCDA 1UAMA 5CO4A 4YQAA 3NK6A 1IPAA 4YVIA 4L69A 4H3YA 3L8UA 4J3CA 4YQ8A 4CNDA 3E5YA 4FAKA 5D9FA 4YQKA 2V3JA 4YQPA 1OY5A 4XBOA 3QUVA 4CNFA 1ZJRA 4YVKA 4X3LA 1Z85A 1P9PA
chains in the Genus database with same CATH homology


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