3BBDA

M. jannaschii nep1 complexed with s-adenosyl-homocysteine
Total Genus 64
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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
64
Knots found
sequence length
204
structure length
204
Chain Sequence
TYNIILAKSALELIPEEIKNKIRKSRVYKYDILDSNYHYKAMEKLKDKEMRGRPDIIHISLLNILDSPINHEKKLNIYIHTYDDKVLKINPETRLPRNYFRFLGVMEKVLKGERNHLIKMEEKTLEDLLNEINAKKIAIMTKTGKLTHPKLLKEYDTFIIGGFPYGKLKINKEKVFGDIKEISIYNKGLMAWTVCGIICYSLSF
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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 Transferase
molecule keywords Ribosome biogenesis protein NEP1-like
publication title The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
pubmed doi rcsb
source organism Methanocaldococcus jannaschii
total genus 64
structure length 204
sequence length 204
chains with identical sequence B
other databases KnotProt 2.0: K +31
ec nomenclature
pdb deposition date 2007-11-09

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 3bbdA00
4YPYA 2YY8A 5GMCA 4YPZA 1VHKA 4YQIA 1K3RA 4YQDA 1UAJA 3ILKA 1V6ZA 4YVIA 1P9PA 1X7OA 4YQBA 3AXZA 4IG6A 1UAKA 4YQ6A 1MXIA 3QUVA 4YPWA 4YPXA 4YQOA 4YQ5A 3NK6A 3IC6A 3KNUA 5GMBA 4CNEA 1UALA 4H3YA 4E8BA 4YQPA 1NXZA 4RG1A 4JALA 4YQLA 1VHYA 4H3ZA 4YQCA 3OIJA 4X3MA 4YQ4A 4J3CA 4MCDA 3OIIA 2QMMA 4YQ8A 4MCCA 3BBHA 3KY7A 4YQAA 1VH0A 1GZ0A 4YQ2A 2O3AA 1TO0A 5FAIA 4YQSA 4YQTA 4YQKA 5GM8A 4YQ1A 4JAKA 4YVJA 4PZKA 1V2XA 4KDZA 4YVKA 3AIAA 4FAKA 3AI9X 1NS5A 2Z0YA 4KGNA 2HA8A 3KTYA 3ONPA 3GYQA 4YQGA 3NK7A 2V3JA 4YQ0A 4YQ9A 2I6DA 5D9FA 3OINA 3IEFA 4L69A 4YQQA 3BBDA 3KW2A 2QWVA 4YQNA 3E5YA 1J85A 4YQ3A 5CO4A 1X7PA 3N4JA 1IPAA 2CX8A 4YVHA 2V3KA 1O6DA 3BBEA 4CNFA 4CNGA 4YQRA 4XBOA 1ZJRA 1UAMA 4YQJA 4MCBA 4YQ7A 3O7BA 1Z85A 4YVGA 3DCMX 4X3LA 2EGWA 1OY5A 3L8UA 4CNDA 2EGVA 3N4KA
chains in the Genus database with same CATH superfamily
4YPYA 2YY8A 5GMCA 4YPZA 1VHKA 4YQIA 4JWHA 1K3RA 4YQDA 1UAJA 3ILKA 1V6ZA 4YVIA 1P9PA 1X7OA 4YQBA 3AXZA 4IG6A 1UAKA 4YQ6A 1MXIA 3QUVA 4YPWA 4YPXA 4YQOA 4YQ5A 3NK6A 3IC6A 3KNUA 5GMBA 4CNEA 1UALA 4H3YA 4E8BA 4YQPA 1NXZA 4RG1A 4JALA 4YQLA 1VHYA 4H3ZA 4YQCA 3OIJA 4X3MA 4YQ4A 4MCDA 4J3CA 3OIIA 2QMMA 4JWGA 4YQ8A 4MCCA 3BBHA 3KY7A 4YQAA 1VH0A 1GZ0A 4YQ2A 2O3AA 1TO0A 5FAIA 4YQSA 4YQTA 4YQKA 5GM8A 4YQ1A 4JAKA 4YVJA 4PZKA 1V2XA 4KDZA 4YVKA 3AIAA 4FAKA 3AI9X 1NS5A 2Z0YA 4FMWA 4KGNA 2HA8A 4JWFA 3KTYA 4JWJA 3ONPA 3GYQA 4YQGA 3NK7A 2V3JA 4YQ0A 4YQ9A 2I6DA 5D9FA 3OINA 3IEFA 4L69A 4YQQA 3BBDA 3KW2A 2QWVA 4YQNA 3E5YA 1J85A 4YQ3A 5CO4A 1X7PA 3N4JA 1IPAA 2CX8A 4YVHA 2V3KA 1O6DA 3BBEA 4CNFA 4CNGA 4YQRA 4XBOA 1ZJRA 1UAMA 4YQJA 4MCBA 4YQ7A 3O7BA 1Z85A 4YVGA 3DCMX 4X3LA 2EGWA 1OY5A 3L8UA 4CNDA 2EGVA 3N4KA
chains in the Genus database with same CATH topology
4YPYA 2YY8A 5GMCA 4YPZA 1VHKA 4YQIA 4JWHA 1K3RA 4YQDA 1UAJA 3ILKA 1V6ZA 4YVIA 1P9PA 1X7OA 4YQBA 3AXZA 4IG6A 1UAKA 4YQ6A 1MXIA 3QUVA 4YPWA 4YPXA 4YQOA 4YQ5A 3NK6A 3IC6A 3KNUA 5GMBA 4CNEA 1UALA 4H3YA 4E8BA 4YQPA 1NXZA 4RG1A 4JALA 4YQLA 1VHYA 4H3ZA 4YQCA 3OIJA 4X3MA 4YQ4A 4MCDA 4J3CA 3OIIA 2QMMA 4JWGA 4YQ8A 4MCCA 3BBHA 3KY7A 4YQAA 1VH0A 1GZ0A 4YQ2A 2O3AA 1TO0A 5FAIA 4YQSA 4YQTA 4YQKA 5GM8A 4YQ1A 4JAKA 4YVJA 4PZKA 1V2XA 4KDZA 4YVKA 3AIAA 4FAKA 3AI9X 1NS5A 2Z0YA 4FMWA 4KGNA 2HA8A 4JWFA 3KTYA 4JWJA 3ONPA 3GYQA 4YQGA 3NK7A 2V3JA 4YQ0A 4YQ9A 2I6DA 5D9FA 3OINA 3IEFA 4L69A 4YQQA 3BBDA 3KW2A 2QWVA 4YQNA 3E5YA 1J85A 4YQ3A 5CO4A 1X7PA 3N4JA 1IPAA 2CX8A 4YVHA 2V3KA 1O6DA 3BBEA 4CNFA 4CNGA 4YQRA 4XBOA 1ZJRA 1UAMA 4YQJA 4MCBA 4YQ7A 3O7BA 1Z85A 4YVGA 3DCMX 4X3LA 2EGWA 1OY5A 3L8UA 4CNDA 2EGVA 3N4KA
chains in the Genus database with same CATH homology


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