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


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