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


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