2QMMA

Crystal structure of apc86534.1 (c-terminal domain of ncbi aab90184.1; pfam big 123.1)
Total Genus 71
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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
71
Knots found
sequence length
195
structure length
195
Chain Sequence
AVRGFLIVGNKAFTQPFSLNDLPGAGRMDVLCRCTSQALFISHGIRRDVEVYLLLLGPPSPPKSILIKGDEVRRMSPDERNVAGHIKKALAVECGKSWKKVHSGVYVSRKGLEELIEELSEKYSIIYLKEDGVDISNAQLPPNPLFVIGDHEGLTEEQEKVVERYAALKLSLSPLSLLAEQCVVIAHHHLDRLQF
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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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publication title Crystal structure of APC86534.1 (C-terminal domain of NCBI AAB90184.1; Pfam BIG 123.1).
rcsb
molecule tags Structural genomics, unknown function
source organism Archaeoglobus fulgidus dsm 4304
molecule keywords UPF0217 protein AF_1056
total genus 71
structure length 195
sequence length 195
chains with identical sequence B
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.257: tRNA (pseudouridine(54)-N(1))-methyltransferase.
pdb deposition date 2007-07-16

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF04013 Methyltrn_RNA_2 Putative SAM-dependent RNA 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 2qmmA00
4YQRA 4YQGA 4YQCA 4E8BA 4YQJA 2HA8A 4YPXA 4JALA 5CO4A 4YQ7A 4YQPA 3KNUA 2O3AA 5FAIA 3IEFA 1ZJRA 3ILKA 3DCMX 4YQIA 3IC6A 4KGNA 3AXZA 1V2XA 3OIJA 2QWVA 5D9FA 4MCBA 1V6ZA 4JAKA 2Z0YA 3E5YA 1VH0A 2QMMA 4CNDA 4YQ4A 4YQQA 2EGWA 4YQ0A 5GMCA 4YQLA 4YQSA 4PZKA 3ONPA 4YQ9A 2EGVA 3OIIA 3AIAA 4J3CA 4YVIA 4CNFA 1K3RA 4YPYA 4YVGA 3GYQA 3KTYA 4YQNA 4YQTA 4H3ZA 4YQ5A 4YQOA 1J85A 1OY5A 3BBHA 4CNGA 1O6DA 3OINA 1GZ0A 2YY8A 3NK7A 1UAMA 1X7PA 4YPWA 1VHKA 2I6DA 4X3LA 4IG6A 4CNEA 3AI9X 4KDZA 3NK6A 4YQDA 4YQ1A 3N4KA 4YVJA 1X7OA 2V3JA 4YPZA 4L69A 4YQ8A 1UALA 4YVHA 5GM8A 2CX8A 4X3MA 4MCDA 3O7BA 3KW2A 4YQ2A 1UAJA 3N4JA 4MCCA 3BBDA 4YQKA 1VHYA 4XBOA 1P9PA 4YQ6A 1MXIA 3QUVA 1TO0A 3KY7A 1Z85A 4YQAA 1IPAA 4YQBA 4YQ3A 5GMBA 3L8UA 4RG1A 1NS5A 2V3KA 3BBEA 1NXZA 4YVKA 4H3YA 1UAKA 4FAKA
chains in the Genus database with same CATH superfamily
4YQRA 4YQGA 4YQCA 4E8BA 4YQJA 2HA8A 4YPXA 4JALA 5CO4A 4YQ7A 4JWJA 4YQPA 3KNUA 2O3AA 5FAIA 3IEFA 1ZJRA 3ILKA 3DCMX 4YQIA 3IC6A 4KGNA 3AXZA 1V2XA 4JWFA 3OIJA 2QWVA 5D9FA 4MCBA 1V6ZA 4JAKA 2Z0YA 3E5YA 4JWGA 1VH0A 2QMMA 4CNDA 4YQ4A 4YQQA 2EGWA 4YQ0A 5GMCA 4YQLA 4YQSA 4PZKA 3ONPA 4YQ9A 2EGVA 3OIIA 3AIAA 4J3CA 4YVIA 4CNFA 1K3RA 4YPYA 4YVGA 3GYQA 3KTYA 4YQNA 4YQTA 4H3ZA 4YQ5A 4FMWA 4YQOA 1J85A 1OY5A 3BBHA 4CNGA 1O6DA 3OINA 1GZ0A 2YY8A 3NK7A 1UAMA 1X7PA 4YPWA 1VHKA 2I6DA 4X3LA 4IG6A 4CNEA 3AI9X 4KDZA 3NK6A 4YQDA 4YQ1A 3N4KA 4YVJA 1X7OA 2V3JA 4YPZA 4L69A 4YQ8A 1UALA 4YVHA 5GM8A 2CX8A 4X3MA 4MCDA 3O7BA 3KW2A 4YQ2A 1UAJA 3N4JA 4MCCA 3BBDA 4YQKA 1VHYA 4XBOA 1P9PA 4YQ6A 1MXIA 3QUVA 1TO0A 3KY7A 1Z85A 4YQAA 1IPAA 4JWHA 4YQBA 4YQ3A 5GMBA 3L8UA 4RG1A 1NS5A 2V3KA 3BBEA 1NXZA 4YVKA 4H3YA 1UAKA 4FAKA
chains in the Genus database with same CATH topology
4YQRA 4YQGA 4YQCA 4E8BA 4YQJA 2HA8A 4YPXA 4JALA 5CO4A 4YQ7A 4JWJA 4YQPA 3KNUA 2O3AA 5FAIA 3IEFA 1ZJRA 3ILKA 3DCMX 4YQIA 3IC6A 4KGNA 3AXZA 1V2XA 4JWFA 3OIJA 2QWVA 5D9FA 4MCBA 1V6ZA 4JAKA 2Z0YA 3E5YA 4JWGA 1VH0A 2QMMA 4CNDA 4YQ4A 4YQQA 2EGWA 4YQ0A 5GMCA 4YQLA 4YQSA 4PZKA 3ONPA 4YQ9A 2EGVA 3OIIA 3AIAA 4J3CA 4YVIA 4CNFA 1K3RA 4YPYA 4YVGA 3GYQA 3KTYA 4YQNA 4YQTA 4H3ZA 4YQ5A 4FMWA 4YQOA 1J85A 1OY5A 3BBHA 4CNGA 1O6DA 3OINA 1GZ0A 2YY8A 3NK7A 1UAMA 1X7PA 4YPWA 1VHKA 2I6DA 4X3LA 4IG6A 4CNEA 3AI9X 4KDZA 3NK6A 4YQDA 4YQ1A 3N4KA 4YVJA 1X7OA 2V3JA 4YPZA 4L69A 4YQ8A 1UALA 4YVHA 5GM8A 2CX8A 4X3MA 4MCDA 3O7BA 3KW2A 4YQ2A 1UAJA 3N4JA 4MCCA 3BBDA 4YQKA 1VHYA 4XBOA 1P9PA 4YQ6A 1MXIA 3QUVA 1TO0A 3KY7A 1Z85A 4YQAA 1IPAA 4JWHA 4YQBA 4YQ3A 5GMBA 3L8UA 4RG1A 1NS5A 2V3KA 3BBEA 1NXZA 4YVKA 4H3YA 1UAKA 4FAKA
chains in the Genus database with same CATH homology


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