3OIJA

Crystal structure of saccharomyces cerevisiae nep1/emg1 bound to s-adenosylhomocysteine and 2 molecules of cognate rna
Total Genus 62
Loading diagram...

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
b'PPVLTSKDKITKRMIVVLAMASLETHKIYVLLNCDDHQGLLDISEARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGILIEVNPTVRIPRTFKRFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHLPTKCRKVTLSFDAPVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYVDEKVGLSNYPLSASVACSKFCHGAEDAWNIL'
Loading diagram...

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


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

 
#similar chains in the Genus database (?% sequence similarity)
...loading similar chains, please wait...
#similar chains, but unknotted
...loading similar chains, please wait...
#similar chains in the pdb database (?% sequence similarity)
...loading similar chains, please wait...