3OINA

Crystal structure of saccharomyces cerevisiae nep1/emg1 bound to s-adenosylhomocysteine and 1 molecule of cognate rna
Total Genus 66
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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
66
Knots found
sequence length
225
structure length
217
Chain Sequence
PPVLTSKDKITKRMIVVLAMASLETHKIKYVLLNCDDHQGLLKKMGRDISEARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGILIEVNPTVRIPRTFKRFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHLPTKCRKVTLSFDAPVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYVDEKVGLSNYPLSASVACSKFCHGAEDAWNIL
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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 66
structure length 217
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 3oinA01
1GZ0A 4YQ1A 4CNDA 3BBEA 3QUVA 1J85A 3AIAA 1X7PA 4YQGA 3KNUA 2V3JA 3N4JA 4X3MA 4YQ8A 1VH0A 5GM8A 5D9FA 3OIIA 1UAMA 3IEFA 4YQ3A 4FAKA 2CX8A 4E8BA 4YQOA 3BBDA 4YPWA 4YQ0A 1NS5A 2QMMA 2O3AA 4YQ4A 1X7OA 4CNFA 1IPAA 4PZKA 4YVGA 4YQCA 4YVKA 2EGVA 5GMCA 1VHYA 4XBOA 4X3LA 4CNEA 3KW2A 1V2XA 4JAKA 2Z0YA 3AI9X 5FAIA 1OY5A 3OINA 3IC6A 2EGWA 3KY7A 3DCMX 4YQAA 1UAKA 4KGNA 3BBHA 4YPZA 4YQDA 4CNGA 5GMBA 4YQRA 4KDZA 3KTYA 3GYQA 4MCCA 1TO0A 4L69A 4YVHA 1UALA 4YQKA 2QWVA 4MCBA 1Z85A 4J3CA 5CO4A 4YQBA 4YQNA 3OIJA 3L8UA 1V6ZA 4YPYA 3ILKA 4YQQA 4YQSA 3ONPA 4YQ9A 1P9PA 3NK7A 4IG6A 4RG1A 4YVJA 4YPXA 1ZJRA 1MXIA 4YQTA 3E5YA 4MCDA 4YQPA 1O6DA 1NXZA 4H3YA 1UAJA 1K3RA 3AXZA 4H3ZA 4YQ6A 4YQ2A 2I6DA 2YY8A 3NK6A 4YQIA 2V3KA 3O7BA 4JALA 1VHKA 4YQ7A 4YQLA 4YQ5A 4YQJA 3N4KA 4YVIA 2HA8A
chains in the Genus database with same CATH superfamily
4JWHA 1GZ0A 4YQ1A 4CNDA 3BBEA 3QUVA 1J85A 3AIAA 1X7PA 4YQGA 3KNUA 2V3JA 3N4JA 4X3MA 4YQ8A 1VH0A 5GM8A 5D9FA 3OIIA 1UAMA 3IEFA 4YQ3A 4FAKA 2CX8A 4E8BA 4YQOA 3BBDA 4JWGA 4YPWA 4YQ0A 1NS5A 2QMMA 2O3AA 4YQ4A 1X7OA 4CNFA 1IPAA 4PZKA 4YVGA 4YQCA 4YVKA 2EGVA 5GMCA 1VHYA 4XBOA 4X3LA 4CNEA 3KW2A 1V2XA 4JAKA 2Z0YA 3AI9X 5FAIA 4FMWA 1OY5A 3OINA 3IC6A 2EGWA 3KY7A 3DCMX 4YQAA 1UAKA 4KGNA 3BBHA 4YPZA 4YQDA 4CNGA 5GMBA 4YQRA 4KDZA 3KTYA 3GYQA 4MCCA 1TO0A 4L69A 4YVHA 1UALA 4YQKA 2QWVA 4MCBA 1Z85A 4J3CA 5CO4A 4YQBA 4YQNA 3OIJA 3L8UA 1V6ZA 4YPYA 3ILKA 4YQQA 4YQSA 3ONPA 4YQ9A 1P9PA 3NK7A 4IG6A 4RG1A 4YVJA 4YPXA 1ZJRA 1MXIA 4YQTA 3E5YA 4MCDA 4YQPA 1O6DA 1NXZA 4H3YA 1UAJA 1K3RA 3AXZA 4H3ZA 4YQ6A 4YQ2A 2I6DA 2YY8A 3NK6A 4YQIA 2V3KA 3O7BA 4JALA 1VHKA 4JWJA 4YQ7A 4YQLA 4JWFA 4YQ5A 4YQJA 3N4KA 4YVIA 2HA8A
chains in the Genus database with same CATH topology
4JWHA 1GZ0A 4YQ1A 4CNDA 3BBEA 3QUVA 1J85A 3AIAA 1X7PA 4YQGA 3KNUA 2V3JA 3N4JA 4X3MA 4YQ8A 1VH0A 5GM8A 5D9FA 3OIIA 1UAMA 3IEFA 4YQ3A 4FAKA 2CX8A 4E8BA 4YQOA 3BBDA 4JWGA 4YPWA 4YQ0A 1NS5A 2QMMA 2O3AA 4YQ4A 1X7OA 4CNFA 1IPAA 4PZKA 4YVGA 4YQCA 4YVKA 2EGVA 5GMCA 1VHYA 4XBOA 4X3LA 4CNEA 3KW2A 1V2XA 4JAKA 2Z0YA 3AI9X 5FAIA 4FMWA 1OY5A 3OINA 3IC6A 2EGWA 3KY7A 3DCMX 4YQAA 1UAKA 4KGNA 3BBHA 4YPZA 4YQDA 4CNGA 5GMBA 4YQRA 4KDZA 3KTYA 3GYQA 4MCCA 1TO0A 4L69A 4YVHA 1UALA 4YQKA 2QWVA 4MCBA 1Z85A 4J3CA 5CO4A 4YQBA 4YQNA 3OIJA 3L8UA 1V6ZA 4YPYA 3ILKA 4YQQA 4YQSA 3ONPA 4YQ9A 1P9PA 3NK7A 4IG6A 4RG1A 4YVJA 4YPXA 1ZJRA 1MXIA 4YQTA 3E5YA 4MCDA 4YQPA 1O6DA 1NXZA 4H3YA 1UAJA 1K3RA 3AXZA 4H3ZA 4YQ6A 4YQ2A 2I6DA 2YY8A 3NK6A 4YQIA 2V3KA 3O7BA 4JALA 1VHKA 4JWJA 4YQ7A 4YQLA 4JWFA 4YQ5A 4YQJA 3N4KA 4YVIA 2HA8A
chains in the Genus database with same CATH homology


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