3OINA

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


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