1NXZA

X-ray crystal structure of protein yggj_haein of haemophilus influenzae. northeast structural genomics consortium target ir73.
Total Genus 67
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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
67
Knots found
sequence length
246
structure length
246
Chain Sequence
RIPRIYHPISLENQTQCYLSEDAANHVARVLRMTEGEQLELFDGSNHIYPAKIIESNKKSVKVEILGRELADKESHLKIHLGQVISRGERMEFTIQKSVELGVNVITPLWSERCGVKLDAERMDKKIQQWQKIAIAACEQCGRNIVPEIRPLMKLQDWCAENDGALKLNLHPRAHYSIKTLPTIPAGGVRLLIGSEGGLSAQEIAQTEQQGFTEILLGKRVLRTETASLAAISALQICFGDLGEAA
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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 Functional assignment based on structural analysis: crystal structure of the yggJ protein (HI0303) of Haemophilus influenzae reveals an RNA methyltransferase with a deep trefoil knot.
pubmed doi rcsb
source organism Haemophilus influenzae
molecule tags Structural genomics, unknown function
molecule keywords Hypothetical protein HI0303
total genus 67
structure length 246
sequence length 246
chains with identical sequence B
other databases KnotProt 2.0: K +31
ec nomenclature ec 2.1.1.193: 16S rRNA (uracil(1498)-N(3))-methyltransferase.
pdb deposition date 2003-02-11

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF04452 Methyltrans_RNA RNA methyltransferase
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.240.20 Mainly Beta Beta Barrel Ribosomal Protein L25; Chain P Hypothetical PUA domain-like; domain 1 1nxzA01
3.40.1280.10 Alpha Beta 3-Layer(aba) Sandwich Alpha/beta knot Alpha/beta knot 1nxzA02
3AXZA 1X7OA 4YQ5A 4YVJA 4YQIA 4MCDA 3KW2A 3BBHA 4YVHA 3NK6A 2NWAA 4KGNA 1GZ0A 4L69A 2I6DA 4YPXA 2YY8A 4CNDA 3L8UA 4YQ4A 4YQ8A 3GYQA 4IG6A 4YVKA 1IPAA 4JAKA 1UAJA 4YQJA 1UAMA 4YQKA 3QUVA 3NK7A 4YVIA 4X3MA 4MCCA 1VH0A 4CNEA 4YQ3A 2Z0YA 4KDZA 4YQCA 1O6DA 3ONPA 1MXIA 4YQ2A 4X3LA 4YQ9A 4YQTA 4YPZA 3OIIA 3IC6A 4XBOA 3IEFA 4YQGA 4PZKA 1P9PA 5GMBA 3N4KA 2O3AA 5FAIA 1UALA 3E5YA 4YQ1A 3AIAA 4RG1A 2QWVA 4YQPA 2HA8A 4FAKA 4YQDA 4E8BA 4H3ZA 4CNFA 4YQ0A 3OIJA 4YQ7A 3N4JA 4YQ6A 1ZJRA 4YQBA 4YQQA 3KY7A 4YVGA 5D9FA 2EGVA 4JALA 2QMMA 4YQLA 1J85A 4CNGA 1OY5A 4YQAA 3ILKA 5CO4A 1TO0A 4YQRA 2EGWA 4MCBA 1V6ZA 4YQOA 4J3CA 1VHKA 2V3KA 3KNUA 4H3YA 4YQSA 3BBEA 4YQNA 4YPYA 1VHYA 1X7PA 3DCMX 1K3RA 1Z85A 1NXZA 1NS5A 3O7BA 2CX8A 1V2XA 3AI9X 5GMCA 3BBDA 1UAKA 2V3JA 3OINA 5GM8A 4YPWA 3KTYA
chains in the Genus database with same CATH superfamily
5JVGS 3PIPS 3AXZA 1X7OA 1O0BA 4H3SA 4YQ5A 4YVJA 2ZJQS 4YQIA 4MCDA 3KW2A 3BBHA 4YVHA 3NK6A 4WFAS 4JWGA 1O0CA 2PJJA 4FMWA 2NWAA 4KGNA 1GZ0A 4L69A 2I6DA 4U67S 4YPXA 2YY8A 5GAHW 4CNDA 3L8UA 2PICA 4H4KA 1EXDA 1QRUA 4YQ4A 4YQ8A 3GYQA 4JYZA 4IG6A 4YVKA 1IPAA 1QRSA 4JAKA 1UAJA 4YQJA 5GAGW 1UAMA 4YQKA 1FEUA 3QUVA 3NK7A 4YVIA 4X3MA 5GAEW 4IOAS 4MCCA 3DLLS 1VH0A 4CNEA 4YQ3A 2Z0YA 2HZ7A 4KDZA 3J7ZV 4YQCA 2GAEA 1O6DA 3ONPA 1MXIA 4YQ2A 4X3LA 4YQ9A 5BNZA 2PI8A 5DM7S 4V194 4YQTA 4YPZA 1GTRA 3OIIA 3X1LB 3IC6A 3IEFA 4XBOA 4YQGA 2PNWA 4PZKA 1B75A 4JWJA 2G5DA 1GTSA 1P9PA 4JWFA 3CZBA 5GMBA 2O3AA 3N4KA 5FAIA 4WFNS 1UALA 2ZJPS 1EUQA 2G6GA 2ZJRS 3E5YA 4YQ1A 3AIAA 4RG1A 3PIOS 2QWVA 3AIIA 2HA8A 4YQPA 4FAKA 4IOCS 4YQDA 4E8BA 4H3ZA 4CNFA 4YQ0A 3OIJA 3CF5S 4YQ7A 3N4JA 4YQ6A 4IO9S 1ZJRA 1QRTA 4P2BA 4YQBA 4YQQA 1EUYA 3KY7A 4YVGA 5HL7S 4WCES 5D9FA 2EGVA 4JALA 2QMMA 1UDXA 4YQLA 1J85A 2AE0X 4CNGA 1OY5A 1NYLA 5DM6S 1DFUP 4YQAA 3ILKA 1ZJWA 4JWHA 1TO0A 5CO4A 2EGWA 2RE8A 4MCBA 4YQRA 1QTQA 1V6ZA 4YQOA 4WF9S 4J3CA 1VHKA 2V3KA 3KNUA 4H3YA 4YQSA 3BBEA 4YQNA 4YPYA 1VHYA 1X7PA 3W2VB 3DCMX 1K3RA 4WFBS 4JXZA 1Z85A 3W2WB 4UY88 2RD2A 1NXZA 1NS5A 3O7BA 2CX8A 1V2XA 3AI9X 5IZNA 5GMCA 3BBDA 1UAKA 2V3JA 1D6KA 3OINA 4JXXA 5GM8A 5GADW 4YPWA 3KTYA 5JVHS
chains in the Genus database with same CATH topology
3AXZA 1X7OA 4YQ5A 4YVJA 4YQIA 4MCDA 3KW2A 3BBHA 4YVHA 3NK6A 4JWGA 4FMWA 2NWAA 4KGNA 1GZ0A 4L69A 2I6DA 4YPXA 2YY8A 4CNDA 3L8UA 4YQ4A 4YQ8A 3GYQA 4IG6A 4YVKA 1IPAA 4JAKA 1UAJA 4YQJA 1UAMA 4YQKA 3QUVA 3NK7A 4YVIA 4X3MA 4MCCA 1VH0A 4CNEA 4YQ3A 2Z0YA 4KDZA 4YQCA 1O6DA 3ONPA 1MXIA 4YQ2A 4X3LA 4YQ9A 4YQTA 4YPZA 3OIIA 3IC6A 4XBOA 3IEFA 4YQGA 4PZKA 4JWJA 1P9PA 4JWFA 5GMBA 3N4KA 2O3AA 5FAIA 1UALA 3E5YA 4YQ1A 3AIAA 4RG1A 2QWVA 4YQPA 2HA8A 4FAKA 4YQDA 4E8BA 4H3ZA 4CNFA 4YQ0A 3OIJA 4YQ7A 3N4JA 4YQ6A 1ZJRA 4YQBA 4YQQA 3KY7A 4YVGA 5D9FA 2EGVA 4JALA 2QMMA 4YQLA 1J85A 4CNGA 1OY5A 4YQAA 3ILKA 5CO4A 4JWHA 1TO0A 4YQRA 2EGWA 4MCBA 1V6ZA 4YQOA 4J3CA 1VHKA 2V3KA 3KNUA 4H3YA 4YQSA 3BBEA 4YQNA 4YPYA 1VHYA 1X7PA 3DCMX 1K3RA 1Z85A 1NXZA 1NS5A 3O7BA 2CX8A 1V2XA 3AI9X 5GMCA 3BBDA 1UAKA 2V3JA 3OINA 5GM8A 4YPWA 3KTYA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 3AXZ A;  1X7O A;  4YQ5 A;  4YVJ A;  4YQI A;  4MCD A;  3KW2 A;  3BBH A;  4YVH A;  3NK6 A;  2NWA A;  4KGN A;  1GZ0 A;  4L69 A;  2I6D A;  4YPX A;  2YY8 A;  4CND A;  3L8U A;  4YQ4 A;  4YQ8 A;  3GYQ A;  4IG6 A;  4YVK A;  1IPA A;  4JAK A;  1UAJ A;  4YQJ A;  1UAM A;  4YQK A;  3QUV A;  3NK7 A;  4YVI A;  4X3M A;  4MCC A;  1VH0 A;  4CNE A;  4YQ3 A;  2Z0Y A;  4KDZ A;  4YQC A;  1O6D A;  3ONP A;  1MXI A;  4YQ2 A;  4X3L A;  4YQ9 A;  4YQT A;  4YPZ A;  3OII A;  3IC6 A;  4XBO A;  3IEF A;  4YQG A;  4PZK A;  1P9P A;  5GMB A;  3N4K A;  2O3A A;  5FAI A;  1UAL A;  3E5Y A;  4YQ1 A;  3AIA A;  4RG1 A;  2QWV A;  4YQP A;  2HA8 A;  4FAK A;  4YQD A;  4E8B A;  4H3Z A;  4CNF A;  4YQ0 A;  3OIJ A;  4YQ7 A;  3N4J A;  4YQ6 A;  1ZJR A;  4YQB A;  4YQQ A;  3KY7 A;  4YVG A;  5D9F A;  2EGV A;  4JAL A;  2QMM A;  4YQL A;  1J85 A;  4CNG A;  1OY5 A;  4YQA A;  3ILK A;  5CO4 A;  1TO0 A;  4YQR A;  2EGW A;  4MCB A;  1V6Z A;  4YQO A;  4J3C A;  1VHK A;  2V3K A;  3KNU A;  4H3Y A;  4YQS A;  3BBE A;  4YQN A;  4YPY A;  1VHY A;  1X7P A;  3DCM X;  1K3R A;  1Z85 A;  1NXZ A;  1NS5 A;  3O7B A;  2CX8 A;  1V2X A;  3AI9 X;  5GMC A;  3BBD A;  1UAK A;  2V3J A;  3OIN A;  5GM8 A;  4YPW A;  3KTY A; 
#chains in the Genus database with same CATH topology
 5JVG S;  3PIP S;  3AXZ A;  1X7O A;  1O0B A;  4H3S A;  4YQ5 A;  4YVJ A;  2ZJQ S;  4YQI A;  4MCD A;  3KW2 A;  3BBH A;  4YVH A;  3NK6 A;  4WFA S;  4JWG A;  1O0C A;  2PJJ A;  4FMW A;  2NWA A;  4KGN A;  1GZ0 A;  4L69 A;  2I6D A;  4U67 S;  4YPX A;  2YY8 A;  5GAH W;  4CND A;  3L8U A;  2PIC A;  4H4K A;  1EXD A;  1QRU A;  4YQ4 A;  4YQ8 A;  3GYQ A;  4JYZ A;  4IG6 A;  4YVK A;  1IPA A;  1QRS A;  4JAK A;  1UAJ A;  4YQJ A;  5GAG W;  1UAM A;  4YQK A;  1FEU A;  3QUV A;  3NK7 A;  4YVI A;  4X3M A;  5GAE W;  4IOA S;  4MCC A;  3DLL S;  1VH0 A;  4CNE A;  4YQ3 A;  2Z0Y A;  2HZ7 A;  4KDZ A;  3J7Z V;  4YQC A;  2GAE A;  1O6D A;  3ONP A;  1MXI A;  4YQ2 A;  4X3L A;  4YQ9 A;  5BNZ A;  2PI8 A;  5DM7 S;  4V19 4;  4YQT A;  4YPZ A;  1GTR A;  3OII A;  3X1L B;  3IC6 A;  3IEF A;  4XBO A;  4YQG A;  2PNW A;  4PZK A;  1B75 A;  4JWJ A;  2G5D A;  1GTS A;  1P9P A;  4JWF A;  3CZB A;  5GMB A;  2O3A A;  3N4K A;  5FAI A;  4WFN S;  1UAL A;  2ZJP S;  1EUQ A;  2G6G A;  2ZJR S;  3E5Y A;  4YQ1 A;  3AIA A;  4RG1 A;  3PIO S;  2QWV A;  3AII A;  2HA8 A;  4YQP A;  4FAK A;  4IOC S;  4YQD A;  4E8B A;  4H3Z A;  4CNF A;  4YQ0 A;  3OIJ A;  3CF5 S;  4YQ7 A;  3N4J A;  4YQ6 A;  4IO9 S;  1ZJR A;  1QRT A;  4P2B A;  4YQB A;  4YQQ A;  1EUY A;  3KY7 A;  4YVG A;  5HL7 S;  4WCE S;  5D9F A;  2EGV A;  4JAL A;  2QMM A;  1UDX A;  4YQL A;  1J85 A;  2AE0 X;  4CNG A;  1OY5 A;  1NYL A;  5DM6 S;  1DFU P;  4YQA A;  3ILK A;  1ZJW A;  4JWH A;  1TO0 A;  5CO4 A;  2EGW A;  2RE8 A;  4MCB A;  4YQR A;  1QTQ A;  1V6Z A;  4YQO A;  4WF9 S;  4J3C A;  1VHK A;  2V3K A;  3KNU A;  4H3Y A;  4YQS A;  3BBE A;  4YQN A;  4YPY A;  1VHY A;  1X7P A;  3W2V B;  3DCM X;  1K3R A;  4WFB S;  4JXZ A;  1Z85 A;  3W2W B;  4UY8 8;  2RD2 A;  1NXZ A;  1NS5 A;  3O7B A;  2CX8 A;  1V2X A;  3AI9 X;  5IZN A;  5GMC A;  3BBD A;  1UAK A;  2V3J A;  1D6K A;  3OIN A;  4JXX A;  5GM8 A;  5GAD W;  4YPW A;  3KTY A;  5JVH S; 
#chains in the Genus database with same CATH homology
 3AXZ A;  1X7O A;  4YQ5 A;  4YVJ A;  4YQI A;  4MCD A;  3KW2 A;  3BBH A;  4YVH A;  3NK6 A;  4JWG A;  4FMW A;  2NWA A;  4KGN A;  1GZ0 A;  4L69 A;  2I6D A;  4YPX A;  2YY8 A;  4CND A;  3L8U A;  4YQ4 A;  4YQ8 A;  3GYQ A;  4IG6 A;  4YVK A;  1IPA A;  4JAK A;  1UAJ A;  4YQJ A;  1UAM A;  4YQK A;  3QUV A;  3NK7 A;  4YVI A;  4X3M A;  4MCC A;  1VH0 A;  4CNE A;  4YQ3 A;  2Z0Y A;  4KDZ A;  4YQC A;  1O6D A;  3ONP A;  1MXI A;  4YQ2 A;  4X3L A;  4YQ9 A;  4YQT A;  4YPZ A;  3OII A;  3IC6 A;  4XBO A;  3IEF A;  4YQG A;  4PZK A;  4JWJ A;  1P9P A;  4JWF A;  5GMB A;  3N4K A;  2O3A A;  5FAI A;  1UAL A;  3E5Y A;  4YQ1 A;  3AIA A;  4RG1 A;  2QWV A;  4YQP A;  2HA8 A;  4FAK A;  4YQD A;  4E8B A;  4H3Z A;  4CNF A;  4YQ0 A;  3OIJ A;  4YQ7 A;  3N4J A;  4YQ6 A;  1ZJR A;  4YQB A;  4YQQ A;  3KY7 A;  4YVG A;  5D9F A;  2EGV A;  4JAL A;  2QMM A;  4YQL A;  1J85 A;  4CNG A;  1OY5 A;  4YQA A;  3ILK A;  5CO4 A;  4JWH A;  1TO0 A;  4YQR A;  2EGW A;  4MCB A;  1V6Z A;  4YQO A;  4J3C A;  1VHK A;  2V3K A;  3KNU A;  4H3Y A;  4YQS A;  3BBE A;  4YQN A;  4YPY A;  1VHY A;  1X7P A;  3DCM X;  1K3R A;  1Z85 A;  1NXZ A;  1NS5 A;  3O7B A;  2CX8 A;  1V2X A;  3AI9 X;  5GMC A;  3BBD A;  1UAK A;  2V3J A;  3OIN A;  5GM8 A;  4YPW A;  3KTY 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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