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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molecule keywords Hypothetical protein HI0303
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
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
2YY8A 2V3KA 4J3CA 5D9FA 4YQDA 1VH0A 4YQGA 3NK7A 1MXIA 3BBHA 3O7BA 4YQIA 4CNEA 3DCMX 4YQSA 4JAKA 2QWVA 3KTYA 4YQ2A 4X3LA 5GMCA 4YVKA 3GYQA 4PZKA 1OY5A 4MCCA 4YVJA 1NS5A 5GM8A 4YQRA 4RG1A 4YQTA 4XBOA 4YQNA 4H3YA 3NK6A 1GZ0A 4IG6A 3KY7A 1O6DA 5GMBA 3OIJA 4YQ3A 4YPYA 4YQPA 4CNDA 3OINA 3AI9X 1TO0A 1UAKA 1P9PA 3BBDA 4YPZA 4E8BA 4YQ8A 3IC6A 4YQCA 4CNFA 5FAIA 3AXZA 1UALA 4YQ1A 3QUVA 1V6ZA 4FAKA 3KNUA 4YQ9A 4YVGA 3AIAA 2O3AA 2CX8A 3KW2A 3L8UA 4CNGA 1VHYA 4YPXA 1X7OA 4YQ0A 4YQ4A 4YQAA 3ILKA 1K3RA 4YQQA 4X3MA 1UAJA 4L69A 4YQ7A 2V3JA 4YQLA 3ONPA 4YPWA 4YQ6A 4YVIA 1NXZA 2QMMA 4YVHA 3IEFA 4KDZA 2I6DA 3N4KA 3N4JA 4YQ5A 4JALA 1Z85A 1VHKA 3BBEA 4MCBA 4KGNA 4YQJA 2EGVA 2NWAA 1ZJRA 4H3ZA 1V2XA 1UAMA 5CO4A 4YQBA 4YQOA 4MCDA 2HA8A 1J85A 3E5YA 3OIIA 1X7PA 1IPAA 2Z0YA 2EGWA 4YQKA
chains in the Genus database with same CATH superfamily
2YY8A 2V3KA 4J3CA 5D9FA 5GAHW 4YQDA 1VH0A 4YQGA 5JVGS 1GTSA 3NK7A 4IOAS 4WFAS 1EUQA 3W2VB 4UY88 4V194 1MXIA 3BBHA 3O7BA 4YQIA 4CNEA 1QRSA 3DCMX 4YQSA 4JAKA 5GAGW 4WCES 3CZBA 2QWVA 3KTYA 4YQ2A 4X3LA 5GMCA 4YVKA 3GYQA 4PZKA 5HL7S 1OY5A 4WF9S 4MCCA 2PI8A 4JXZA 1NS5A 2PJJA 4YVJA 5GM8A 2ZJRS 4YQRA 4RG1A 3J7ZV 5DM6S 4YQTA 4XBOA 4YQNA 4H3YA 3NK6A 1GZ0A 4IG6A 3KY7A 1O6DA 5GMBA 3OIJA 4YQ3A 4JXXA 4YPYA 4YQPA 4CNDA 3OINA 3AI9X 1TO0A 1UAKA 1QRTA 1P9PA 3BBDA 4YPZA 4E8BA 4JYZA 4YQ8A 3DLLS 3IC6A 4YQCA 4CNFA 5FAIA 3AXZA 3CF5S 1QRUA 1UALA 4YQ1A 4P2BA 1V6ZA 3QUVA 4WFBS 4FAKA 2ZJPS 3KNUA 2ZJQS 4JWGA 1O0BA 1O0CA 4YVGA 4JWJA 4YQ9A 3AIAA 4H3SA 2O3AA 4JWHA 2CX8A 3KW2A 1B75A 4U67S 2GAEA 2AE0X 4WFNS 3L8UA 2HZ7A 4IOCS 3W2WB 4CNGA 1VHYA 2PNWA 4YPXA 2G5DA 1FEUA 1X7OA 4YQ0A 4YQ4A 2G6GA 1DFUP 4YQAA 3ILKA 1K3RA 1D6KA 4H4KA 1GTRA 4X3MA 4YQQA 1UAJA 4L69A 4YQ7A 2V3JA 4FMWA 3PIPS 2PICA 4YQLA 5IZNA 3ONPA 1ZJWA 4YPWA 4YQ6A 4YVIA 1NXZA 2RD2A 2QMMA 4YVHA 3IEFA 4KDZA 2I6DA 3N4KA 3N4JA 4YQ5A 1UDXA 1Z85A 1VHKA 5GADW 3BBEA 4JALA 4KGNA 4MCBA 4YQJA 3PIOS 2EGVA 2NWAA 5BNZA 1ZJRA 4H3ZA 1V2XA 1UAMA 4IO9S 1QTQA 5CO4A 4YQBA 4YQOA 4MCDA 2HA8A 1J85A 5GAEW 1EXDA 3E5YA 3OIIA 3AIIA 1NYLA 1X7PA 4JWFA 1IPAA 3X1LB 1EUYA 5DM7S 2RE8A 5JVHS 2Z0YA 2EGWA 4YQKA
chains in the Genus database with same CATH topology
2YY8A 2V3KA 4J3CA 5D9FA 4YQDA 1VH0A 4YQGA 3NK7A 1MXIA 3BBHA 3O7BA 4YQIA 4CNEA 3DCMX 4YQSA 4JAKA 2QWVA 3KTYA 4YQ2A 4X3LA 5GMCA 4YVKA 3GYQA 4PZKA 1OY5A 4MCCA 4YVJA 1NS5A 5GM8A 4YQRA 4RG1A 4YQTA 4XBOA 4YQNA 4H3YA 3NK6A 1GZ0A 4IG6A 3KY7A 1O6DA 5GMBA 3OIJA 4YQ3A 4YPYA 4YQPA 4CNDA 3OINA 3AI9X 1TO0A 1UAKA 1P9PA 3BBDA 4YPZA 4E8BA 4YQ8A 3IC6A 4YQCA 4CNFA 5FAIA 3AXZA 1UALA 4YQ1A 3QUVA 1V6ZA 4FAKA 3KNUA 4JWGA 4YQ9A 4YVGA 4JWJA 3AIAA 2O3AA 4JWHA 2CX8A 3KW2A 3L8UA 4CNGA 1VHYA 4YPXA 1X7OA 4YQ0A 4YQ4A 4YQAA 3ILKA 1K3RA 4YQQA 4X3MA 1UAJA 4L69A 4YQ7A 2V3JA 4FMWA 4YQLA 3ONPA 4YPWA 4YQ6A 4YVIA 1NXZA 2QMMA 4YVHA 3IEFA 4KDZA 2I6DA 3N4KA 3N4JA 4YQ5A 4JALA 1Z85A 1VHKA 3BBEA 4MCBA 4KGNA 4YQJA 2EGVA 2NWAA 1ZJRA 4H3ZA 1V2XA 1UAMA 5CO4A 4YQBA 4YQOA 4MCDA 2HA8A 1J85A 3E5YA 3OIIA 1X7PA 4JWFA 1IPAA 2Z0YA 2EGWA 4YQKA
chains in the Genus database with same CATH homology


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