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


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

 
#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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