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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molecule tags Structural genomics, unknown function
molecule keywords UPF0217 protein AF_1056
publication title Crystal structure of APC86534.1 (C-terminal domain of NCBI AAB90184.1; Pfam BIG 123.1).
rcsb
source organism Archaeoglobus fulgidus dsm 4304
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
4YQ7A 1VHKA 4YQDA 1TO0A 4KGNA 4E8BA 3KNUA 2V3KA 4YPZA 2V3JA 1IPAA 1NXZA 4CNDA 4JALA 1OY5A 1Z85A 4YQSA 3E5YA 1ZJRA 5GMCA 4CNFA 4X3LA 4CNEA 1UALA 3ONPA 4X3MA 3QUVA 4YQQA 2EGWA 3KW2A 1X7OA 1UAKA 4YQNA 3BBDA 1UAMA 1VH0A 4YQIA 4MCCA 4YQAA 1O6DA 4MCDA 3L8UA 4YQ8A 3DCMX 2QWVA 4YQKA 4YQPA 4YQOA 4YQ1A 2YY8A 3IC6A 4YQCA 4YQ2A 1J85A 3KTYA 4YQ9A 4YPYA 4MCBA 3KY7A 4YPXA 1UAJA 4YQ3A 3ILKA 4IG6A 3BBEA 1VHYA 2HA8A 4YQJA 4YVGA 2CX8A 1GZ0A 1X7PA 2O3AA 2Z0YA 5CO4A 4YQ4A 4YQBA 3OIIA 3N4JA 4YQ5A 2EGVA 4J3CA 1MXIA 4RG1A 3OINA 4JAKA 3O7BA 3OIJA 4PZKA 1K3RA 4YPWA 3AIAA 4XBOA 5GM8A 3IEFA 4YQLA 4YVJA 4YQ0A 4H3ZA 5D9FA 5FAIA 4FAKA 3NK6A 4YQGA 4YQRA 1V6ZA 1P9PA 4YVHA 4KDZA 4YVIA 3GYQA 4YVKA 3N4KA 4YQ6A 3NK7A 3AXZA 2I6DA 4L69A 4YQTA 1V2XA 1NS5A 5GMBA 3BBHA 2QMMA 3AI9X 4CNGA 4H3YA
chains in the Genus database with same CATH superfamily
4YQ7A 1VHKA 4YQDA 1TO0A 4KGNA 4E8BA 3KNUA 2V3KA 4YPZA 2V3JA 1IPAA 1NXZA 4FMWA 4CNDA 4JALA 1OY5A 1Z85A 4JWGA 4YQSA 3E5YA 1ZJRA 5GMCA 4CNFA 4X3LA 4JWFA 4CNEA 1UALA 3ONPA 4X3MA 3QUVA 4YQQA 2EGWA 3KW2A 1X7OA 1UAKA 4YQNA 3BBDA 1UAMA 1VH0A 4YQIA 4MCCA 4YQAA 1O6DA 4MCDA 3L8UA 4YQ8A 3DCMX 2QWVA 4YQKA 4YQPA 4YQOA 4YQ1A 2YY8A 3IC6A 4YQCA 4YQ2A 1J85A 3KTYA 4YQ9A 4YPYA 4MCBA 3KY7A 4YPXA 1UAJA 4YQ3A 3ILKA 4IG6A 3BBEA 1VHYA 2HA8A 4YQJA 4YVGA 2CX8A 1GZ0A 1X7PA 2O3AA 2Z0YA 5CO4A 4YQ4A 4YQBA 3OIIA 3N4JA 4YQ5A 2EGVA 4J3CA 1MXIA 4RG1A 3OINA 4JAKA 3O7BA 3OIJA 4PZKA 1K3RA 4YPWA 3AIAA 4XBOA 5GM8A 3IEFA 4YQLA 4YVJA 4YQ0A 4H3ZA 5D9FA 5FAIA 4FAKA 3NK6A 4YQGA 4YQRA 1V6ZA 1P9PA 4YVHA 4KDZA 4YVIA 4JWJA 3GYQA 4YVKA 3N4KA 4YQ6A 3NK7A 3AXZA 2I6DA 4JWHA 4L69A 4YQTA 1V2XA 1NS5A 5GMBA 3BBHA 2QMMA 3AI9X 4CNGA 4H3YA
chains in the Genus database with same CATH topology
4YQ7A 1VHKA 4YQDA 1TO0A 4KGNA 4E8BA 3KNUA 2V3KA 4YPZA 2V3JA 1IPAA 1NXZA 4FMWA 4CNDA 4JALA 1OY5A 1Z85A 4JWGA 4YQSA 3E5YA 1ZJRA 5GMCA 4CNFA 4X3LA 4JWFA 4CNEA 1UALA 3ONPA 4X3MA 3QUVA 4YQQA 2EGWA 3KW2A 1X7OA 1UAKA 4YQNA 3BBDA 1UAMA 1VH0A 4YQIA 4MCCA 4YQAA 1O6DA 4MCDA 3L8UA 4YQ8A 3DCMX 2QWVA 4YQKA 4YQPA 4YQOA 4YQ1A 2YY8A 3IC6A 4YQCA 4YQ2A 1J85A 3KTYA 4YQ9A 4YPYA 4MCBA 3KY7A 4YPXA 1UAJA 4YQ3A 3ILKA 4IG6A 3BBEA 1VHYA 2HA8A 4YQJA 4YVGA 2CX8A 1GZ0A 1X7PA 2O3AA 2Z0YA 5CO4A 4YQ4A 4YQBA 3OIIA 3N4JA 4YQ5A 2EGVA 4J3CA 1MXIA 4RG1A 3OINA 4JAKA 3O7BA 3OIJA 4PZKA 1K3RA 4YPWA 3AIAA 4XBOA 5GM8A 3IEFA 4YQLA 4YVJA 4YQ0A 4H3ZA 5D9FA 5FAIA 4FAKA 3NK6A 4YQGA 4YQRA 1V6ZA 1P9PA 4YVHA 4KDZA 4YVIA 4JWJA 3GYQA 4YVKA 3N4KA 4YQ6A 3NK7A 3AXZA 2I6DA 4JWHA 4L69A 4YQTA 1V2XA 1NS5A 5GMBA 3BBHA 2QMMA 3AI9X 4CNGA 4H3YA
chains in the Genus database with same CATH homology


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