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


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