3BBEA

M. jannaschii nep1
Total Genus 70
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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
70
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 70
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 3bbeA00
3NK7A 4YPWA 3DCMX 4J3CA 5GM8A 1X7OA 1P9PA 2V3KA 2O3AA 4X3LA 3OINA 1Z85A 1X7PA 3AIAA 4YQ7A 1ZJRA 2HA8A 4YPZA 2Z0YA 4YQIA 1VHKA 4L69A 3KW2A 4CNFA 4YQ9A 3O7BA 1K3RA 5CO4A 3IEFA 4YVJA 4H3YA 1MXIA 3QUVA 4YVHA 4YPXA 3KNUA 3OIIA 4YQRA 5GMCA 5GMBA 4YQQA 4YQPA 4YQ4A 1UAKA 4YQ8A 3L8UA 1TO0A 1IPAA 4FAKA 1OY5A 4YQCA 3N4JA 4XBOA 4YQ2A 4YQJA 1UAMA 2QMMA 4CNDA 4YQNA 2QWVA 4YQLA 3N4KA 4YQ0A 3BBHA 2YY8A 3GYQA 4YVGA 2EGVA 3ILKA 1V2XA 4PZKA 4YQ1A 3IC6A 4YVIA 4MCCA 3OIJA 4CNGA 4JALA 4YQKA 2V3JA 4IG6A 1O6DA 2EGWA 5D9FA 5FAIA 4JAKA 3AI9X 4E8BA 3KTYA 1UAJA 4YQAA 4YPYA 4YQ3A 4MCDA 4H3ZA 4RG1A 4YQTA 4KGNA 4YQDA 4YQOA 1VH0A 3KY7A 2I6DA 3E5YA 1UALA 1NXZA 1GZ0A 4YQGA 4CNEA 4YQBA 2CX8A 1J85A 4YQ6A 1NS5A 3AXZA 4YVKA 1VHYA 4MCBA 3BBDA 3NK6A 4YQSA 3BBEA 4KDZA 4X3MA 4YQ5A 3ONPA 1V6ZA
chains in the Genus database with same CATH superfamily
3NK7A 4YPWA 3DCMX 4J3CA 4FMWA 5GM8A 1X7OA 1P9PA 2V3KA 2O3AA 4X3LA 3OINA 1Z85A 1X7PA 3AIAA 4YQ7A 1ZJRA 2HA8A 4YPZA 2Z0YA 4YQIA 1VHKA 4L69A 3KW2A 4CNFA 4YQ9A 3O7BA 1K3RA 5CO4A 3IEFA 4YVJA 4H3YA 1MXIA 3QUVA 4YVHA 4YPXA 3KNUA 4JWFA 3OIIA 4JWJA 4YQRA 5GMCA 5GMBA 4YQQA 4YQPA 4YQ4A 4JWGA 1UAKA 4YQ8A 3L8UA 1TO0A 1IPAA 4FAKA 1OY5A 4YQCA 3N4JA 4XBOA 4YQ2A 4YQJA 1UAMA 2QMMA 4CNDA 4YQNA 2QWVA 4YQLA 3N4KA 4YQ0A 3BBHA 4JWHA 2YY8A 3GYQA 4YVGA 2EGVA 3ILKA 1V2XA 4PZKA 4YQ1A 3IC6A 4YVIA 4MCCA 3OIJA 4CNGA 4JALA 4YQKA 2V3JA 4IG6A 1O6DA 2EGWA 5D9FA 5FAIA 4JAKA 3AI9X 4E8BA 3KTYA 1UAJA 4YQAA 4YPYA 4YQ3A 4MCDA 4H3ZA 4RG1A 4YQTA 4KGNA 4YQDA 4YQOA 1VH0A 3KY7A 2I6DA 3E5YA 1UALA 1NXZA 1GZ0A 4YQGA 4CNEA 4YQBA 2CX8A 1J85A 4YQ6A 1NS5A 3AXZA 4YVKA 1VHYA 4MCBA 3BBDA 3NK6A 4YQSA 3BBEA 4KDZA 4X3MA 4YQ5A 3ONPA 1V6ZA
chains in the Genus database with same CATH topology
3NK7A 4YPWA 3DCMX 4J3CA 4FMWA 5GM8A 1X7OA 1P9PA 2V3KA 2O3AA 4X3LA 3OINA 1Z85A 1X7PA 3AIAA 4YQ7A 1ZJRA 2HA8A 4YPZA 2Z0YA 4YQIA 1VHKA 4L69A 3KW2A 4CNFA 4YQ9A 3O7BA 1K3RA 5CO4A 3IEFA 4YVJA 4H3YA 1MXIA 3QUVA 4YVHA 4YPXA 3KNUA 4JWFA 3OIIA 4JWJA 4YQRA 5GMCA 5GMBA 4YQQA 4YQPA 4YQ4A 4JWGA 1UAKA 4YQ8A 3L8UA 1TO0A 1IPAA 4FAKA 1OY5A 4YQCA 3N4JA 4XBOA 4YQ2A 4YQJA 1UAMA 2QMMA 4CNDA 4YQNA 2QWVA 4YQLA 3N4KA 4YQ0A 3BBHA 4JWHA 2YY8A 3GYQA 4YVGA 2EGVA 3ILKA 1V2XA 4PZKA 4YQ1A 3IC6A 4YVIA 4MCCA 3OIJA 4CNGA 4JALA 4YQKA 2V3JA 4IG6A 1O6DA 2EGWA 5D9FA 5FAIA 4JAKA 3AI9X 4E8BA 3KTYA 1UAJA 4YQAA 4YPYA 4YQ3A 4MCDA 4H3ZA 4RG1A 4YQTA 4KGNA 4YQDA 4YQOA 1VH0A 3KY7A 2I6DA 3E5YA 1UALA 1NXZA 1GZ0A 4YQGA 4CNEA 4YQBA 2CX8A 1J85A 4YQ6A 1NS5A 3AXZA 4YVKA 1VHYA 4MCBA 3BBDA 3NK6A 4YQSA 3BBEA 4KDZA 4X3MA 4YQ5A 3ONPA 1V6ZA
chains in the Genus database with same CATH homology


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