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


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