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


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