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


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