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


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