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


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