1J85A

Structure of yibk from haemophilus influenzae (hi0766), a truncated sequence homolog of trna (guanosine-2'-o-) methyltransferase (spou)
Total Genus 44

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
44
Knots found
sequence length
156
structure length
156
Chain Sequence
MLDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESEKPKRLFALTTKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAWRQLGYKGAVNL

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
S2 (28-32)TIV1 (6-9)TI4 (101-104)EMPTYAH1 (12-25)3H1 (51-53)S3 (57-60)TI1 (38-41)AH2 (42-46)TIV2 (46-49)TIV3 (54-57)AH3 (63-70)S5 (95-99)S4 (74-78)3H2 (116-118)S6 (119-120)TI2 (79-82)TI3 (85-88)AH5 (133-148)TIV4 (86-89)TII1 (92-95)AH4 (108-112)TIV5 (125-128)TII2 (150-153)TIV6 (148-151)S1 (3-7)Updating...
connected with : NaN
publication title Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot
pubmed doi rcsb
molecule keywords YibK
molecule tags Transferase
source organism Haemophilus influenzae rd
total genus 44
structure length 156
sequence length 156
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.207: tRNA (cytidine(34)-2'-O)-methyltransferase.
pdb deposition date 2001-05-20

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00588 SpoU_methylase SpoU rRNA Methylase family
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 1j85A00
3BBDA 2O3AA 4YQIA 2QWVA 4YQ6A 1UALA 1NS5A 3NK7A 3O7BA 4H3YA 4H3ZA 4J3CA 5FAIA 4YVHA 3IEFA 1X7PA 4L69A 4MCDA 4X3LA 4YQRA 4PZKA 4YQKA 4CNDA 4JALA 4CNEA 1O6DA 1MXIA 1VH0A 3N4JA 4YQ2A 4YQ4A 3N4KA 4FAKA 1UAKA 3KNUA 4YQ0A 1J85A 3AXZA 1UAMA 4YQGA 1P9PA 1VHYA 3KW2A 4YVGA 4CNFA 5GMCA 1X7OA 4YQ7A 2EGWA 4YPWA 5GM8A 4YQ1A 2YY8A 3KTYA 4YQAA 1IPAA 2QMMA 3QUVA 5CO4A 2I6DA 1OY5A 4XBOA 4MCBA 4YQSA 4YVKA 4KGNA 4YQNA 1VHKA 4MCCA 4YQPA 3BBEA 3KY7A 2Z0YA 4YQ8A 3DCMX 2CX8A 4YQCA 3ONPA 1TO0A 4E8BA 1Z85A 3AIAA 4IG6A 2EGVA 4YQDA 4YQLA 3L8UA 3OIIA 3OIJA 3AI9X 4YPXA 3ILKA 4RG1A 4YQQA 5D9FA 4YPZA 4YQTA 3IC6A 5GMBA 3BBHA 1ZJRA 1V6ZA 4YVJA 1GZ0A 1V2XA 4YQ5A 3OINA 4X3MA 4YVIA 2V3JA 3GYQA 4YPYA 1NXZA 4YQ3A 4YQOA 2HA8A 3E5YA 4YQJA 3NK6A 4YQBA 2V3KA 4YQ9A 4CNGA 1K3RA 4JAKA 1UAJA 4KDZA
chains in the Genus database with same CATH superfamily
3BBDA 2O3AA 4YQIA 2QWVA 4YQ6A 1UALA 1NS5A 3NK7A 3O7BA 4H3YA 4H3ZA 4J3CA 5FAIA 4YVHA 3IEFA 1X7PA 4L69A 4MCDA 4X3LA 4YQRA 4PZKA 4YQKA 4CNDA 4JALA 4CNEA 1O6DA 1MXIA 1VH0A 3N4JA 4YQ2A 4YQ4A 3N4KA 4FAKA 1UAKA 3KNUA 4YQ0A 1J85A 3AXZA 1UAMA 4YQGA 1P9PA 1VHYA 3KW2A 4YVGA 4CNFA 5GMCA 1X7OA 4YQ7A 2EGWA 4JWJA 4YPWA 4JWHA 5GM8A 4YQ1A 2YY8A 3KTYA 4YQAA 1IPAA 2QMMA 3QUVA 5CO4A 2I6DA 1OY5A 4XBOA 4MCBA 4YQSA 4JWFA 4YVKA 4JWGA 4KGNA 4YQNA 1VHKA 4MCCA 4YQPA 3BBEA 3KY7A 4FMWA 2Z0YA 4YQ8A 3DCMX 2CX8A 4YQCA 3ONPA 1TO0A 4E8BA 1Z85A 3AIAA 4IG6A 2EGVA 4YQDA 4YQLA 3L8UA 3OIIA 3OIJA 3AI9X 4YPXA 3ILKA 4RG1A 4YQQA 5D9FA 4YPZA 4YQTA 3IC6A 5GMBA 3BBHA 1ZJRA 1V6ZA 4YVJA 1GZ0A 1V2XA 4YQ5A 3OINA 4X3MA 4YVIA 2V3JA 3GYQA 4YPYA 1NXZA 4YQ3A 4YQOA 2HA8A 3E5YA 4YQJA 3NK6A 4YQBA 2V3KA 4YQ9A 4CNGA 1K3RA 4JAKA 1UAJA 4KDZA
chains in the Genus database with same CATH topology
3BBDA 2O3AA 4YQIA 2QWVA 4YQ6A 1UALA 1NS5A 3NK7A 3O7BA 4H3YA 4H3ZA 4J3CA 5FAIA 4YVHA 3IEFA 1X7PA 4L69A 4MCDA 4X3LA 4YQRA 4PZKA 4YQKA 4CNDA 4JALA 4CNEA 1O6DA 1MXIA 1VH0A 3N4JA 4YQ2A 4YQ4A 3N4KA 4FAKA 1UAKA 3KNUA 4YQ0A 1J85A 3AXZA 1UAMA 4YQGA 1P9PA 1VHYA 3KW2A 4YVGA 4CNFA 5GMCA 1X7OA 4YQ7A 2EGWA 4JWJA 4YPWA 4JWHA 5GM8A 4YQ1A 2YY8A 3KTYA 4YQAA 1IPAA 2QMMA 3QUVA 5CO4A 2I6DA 1OY5A 4XBOA 4MCBA 4YQSA 4JWFA 4YVKA 4JWGA 4KGNA 4YQNA 1VHKA 4MCCA 4YQPA 3BBEA 3KY7A 4FMWA 2Z0YA 4YQ8A 3DCMX 2CX8A 4YQCA 3ONPA 1TO0A 4E8BA 1Z85A 3AIAA 4IG6A 2EGVA 4YQDA 4YQLA 3L8UA 3OIIA 3OIJA 3AI9X 4YPXA 3ILKA 4RG1A 4YQQA 5D9FA 4YPZA 4YQTA 3IC6A 5GMBA 3BBHA 1ZJRA 1V6ZA 4YVJA 1GZ0A 1V2XA 4YQ5A 3OINA 4X3MA 4YVIA 2V3JA 3GYQA 4YPYA 1NXZA 4YQ3A 4YQOA 2HA8A 3E5YA 4YQJA 3NK6A 4YQBA 2V3KA 4YQ9A 4CNGA 1K3RA 4JAKA 1UAJA 4KDZA
chains in the Genus database with same CATH homology


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

 
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#similar chains, but unknotted
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