3BM2A

Crystal structure of a minimal nitroreductase ydja from escherichia coli k12 with and without fmn cofactor
Total Genus 33
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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
33
sequence length
184
structure length
165
Chain Sequence
MDALELLINRRSASRLAEPAPTGEQLQNILRAGMRAQPWHFFVIEGEGRERFSAVLEQGAIAAGSDDKAIDKARNAPFRAPLIITVVAKCEQEMSAGCAVMAMQMAAVAQGFGGIWRSGALTESPVVREAFGCREQDKIVGFLYLGTPQLSINVPDPTPFVTYFH
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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 Oxidoreductase
molecule keywords Protein ydjA
publication title Crystal structure of a minimal nitroreductase, ydjA, from Escherichia coli K12 with and without FMN cofactor
pubmed doi rcsb
source organism Escherichia coli
total genus 33
structure length 165
sequence length 184
chains with identical sequence B
ec nomenclature ec 1.5.1.34: 6,7-dihydropteridine reductase.
pdb deposition date 2007-12-12

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF00881 Nitroreductase Nitroreductase family
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
3.40.109.10 Alpha Beta 3-Layer(aba) Sandwich NADH Oxidase NADH Oxidase 3bm2A00
1KQBA 3BM1A 4BNBA 2IFAA 3M5KA 1YKIA 3X21A 3E10A 4TTCA 2FREA 3GB5A 3GR3A 3EOFA 3EO8A 4BN7A 3OF4A 2ISJA 1ZCHA 1ICUA 3H4OA 5KO7A 1KQCA 3QDLA 1OOQA 4QLXA 5HEIA 3GFAA 4BN6A 3G14A 3GH8A 1YWQA 1OONA 3BM2A 1OO5A 3KOQA 2R01A 3GBHA 5J6CA 1BKJA 2WZVA 1V5ZA 1YLRA 4DN2A 1F5VA 1V5YA 4XOMA 2ISKA 3E39A 3GE5A 3HZNA 4QLYA 1DS7A 2WZWA 4EO3A 4XOQA 3BEMA 1YLUA 3HJ9A 3EK3A 1VFRA 3K6HA 2YMVA 1ICVA 3PXVA 3GE6A 1ICRA 1VKWA 5KO8A 2HAYA 2BKJA 2WQFA 4BN9A 3TO0A 3EO7A 3TNZA 2I7HA 3X22A 3N2SA 1OO6A 4G8SA 1IDTA 5HDJA 5KRDA 3GFDA 1NECA 3HOIA 2H0UA 2ISLA 4XOOA 1NOXA 1KQDA 4TTBA 3KWKA 4URPA 4BN8A 3GAGA 2B67A
chains in the Genus database with same CATH superfamily
1KQBA 3BM1A 4BNBA 2IFAA 3M5KA 1YKIA 3X21A 3E10A 4TTCA 2FREA 3GB5A 3GR3A 3EOFA 3EO8A 4BN7A 3OF4A 2ISJA 1ZCHA 1ICUA 3H4OA 5KO7A 1KQCA 3QDLA 1OOQA 4QLXA 5HEIA 3GFAA 4BN6A 3G14A 3GH8A 1YWQA 1J6RA 1OONA 3BM2A 1OO5A 3KOQA 2R01A 3GBHA 5J6CA 1BKJA 2WZVA 1V5ZA 1YLRA 4DN2A 1F5VA 1V5YA 4XOMA 2ISKA 3E39A 3GE5A 3HZNA 4QLYA 1DS7A 2WZWA 4EO3A 4XOQA 3BEMA 1YLUA 3HJ9A 3EK3A 1VFRA 3K6HA 2YMVA 1ICVA 3PXVA 3GE6A 1ICRA 1VKWA 5KO8A 2HAYA 2BKJA 2WQFA 4BN9A 3TO0A 3EO7A 3TNZA 2I7HA 3X22A 3N2SA 1OO6A 4G8SA 1IDTA 5HDJA 5KRDA 3GFDA 1NECA 3HOIA 2H0UA 2ISLA 4XOOA 1NOXA 1KQDA 4TTBA 3KWKA 4URPA 4BN8A 3GAGA 2B67A
chains in the Genus database with same CATH topology
1KQBA 3BM1A 4BNBA 2IFAA 3M5KA 1YKIA 3X21A 3E10A 4TTCA 2FREA 3GB5A 3GR3A 3EOFA 3EO8A 4BN7A 3OF4A 2ISJA 1ZCHA 1ICUA 3H4OA 5KO7A 1KQCA 3QDLA 1OOQA 4QLXA 5HEIA 3GFAA 4BN6A 3G14A 3GH8A 1YWQA 1J6RA 1OONA 3BM2A 1OO5A 3KOQA 2R01A 3GBHA 5J6CA 1BKJA 2WZVA 1V5ZA 1YLRA 4DN2A 1F5VA 1V5YA 4XOMA 2ISKA 3E39A 3GE5A 3HZNA 4QLYA 1DS7A 2WZWA 4EO3A 4XOQA 3BEMA 1YLUA 3HJ9A 3EK3A 1VFRA 3K6HA 2YMVA 1ICVA 3PXVA 3GE6A 1ICRA 1VKWA 5KO8A 2HAYA 2BKJA 2WQFA 4BN9A 3TO0A 3EO7A 3TNZA 2I7HA 3X22A 3N2SA 1OO6A 4G8SA 1IDTA 5HDJA 5KRDA 3GFDA 1NECA 3HOIA 2H0UA 2ISLA 4XOOA 1NOXA 1KQDA 4TTBA 3KWKA 4URPA 4BN8A 3GAGA 2B67A
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 1KQB A;  3BM1 A;  4BNB A;  2IFA A;  3M5K A;  1YKI A;  3X21 A;  3E10 A;  4TTC A;  2FRE A;  3GB5 A;  3GR3 A;  3EOF A;  3EO8 A;  4BN7 A;  3OF4 A;  2ISJ A;  1ZCH A;  1ICU A;  3H4O A;  5KO7 A;  1KQC A;  3QDL A;  1OOQ A;  4QLX A;  5HEI A;  3GFA A;  4BN6 A;  3G14 A;  3GH8 A;  1YWQ A;  1OON A;  3BM2 A;  1OO5 A;  3KOQ A;  2R01 A;  3GBH A;  5J6C A;  1BKJ A;  2WZV A;  1V5Z A;  1YLR A;  4DN2 A;  1F5V A;  1V5Y A;  4XOM A;  2ISK A;  3E39 A;  3GE5 A;  3HZN A;  4QLY A;  1DS7 A;  2WZW A;  4EO3 A;  4XOQ A;  3BEM A;  1YLU A;  3HJ9 A;  3EK3 A;  1VFR A;  3K6H A;  2YMV A;  1ICV A;  3PXV A;  3GE6 A;  1ICR A;  1VKW A;  5KO8 A;  2HAY A;  2BKJ A;  2WQF A;  4BN9 A;  3TO0 A;  3EO7 A;  3TNZ A;  2I7H A;  3X22 A;  3N2S A;  1OO6 A;  4G8S A;  1IDT A;  5HDJ A;  5KRD A;  3GFD A;  1NEC A;  3HOI A;  2H0U A;  2ISL A;  4XOO A;  1NOX A;  1KQD A;  4TTB A;  3KWK A;  4URP A;  4BN8 A;  3GAG A;  2B67 A; 
#chains in the Genus database with same CATH topology
 1KQB A;  3BM1 A;  4BNB A;  2IFA A;  3M5K A;  1YKI A;  3X21 A;  3E10 A;  4TTC A;  2FRE A;  3GB5 A;  3GR3 A;  3EOF A;  3EO8 A;  4BN7 A;  3OF4 A;  2ISJ A;  1ZCH A;  1ICU A;  3H4O A;  5KO7 A;  1KQC A;  3QDL A;  1OOQ A;  4QLX A;  5HEI A;  3GFA A;  4BN6 A;  3G14 A;  3GH8 A;  1YWQ A;  1J6R A;  1OON A;  3BM2 A;  1OO5 A;  3KOQ A;  2R01 A;  3GBH A;  5J6C A;  1BKJ A;  2WZV A;  1V5Z A;  1YLR A;  4DN2 A;  1F5V A;  1V5Y A;  4XOM A;  2ISK A;  3E39 A;  3GE5 A;  3HZN A;  4QLY A;  1DS7 A;  2WZW A;  4EO3 A;  4XOQ A;  3BEM A;  1YLU A;  3HJ9 A;  3EK3 A;  1VFR A;  3K6H A;  2YMV A;  1ICV A;  3PXV A;  3GE6 A;  1ICR A;  1VKW A;  5KO8 A;  2HAY A;  2BKJ A;  2WQF A;  4BN9 A;  3TO0 A;  3EO7 A;  3TNZ A;  2I7H A;  3X22 A;  3N2S A;  1OO6 A;  4G8S A;  1IDT A;  5HDJ A;  5KRD A;  3GFD A;  1NEC A;  3HOI A;  2H0U A;  2ISL A;  4XOO A;  1NOX A;  1KQD A;  4TTB A;  3KWK A;  4URP A;  4BN8 A;  3GAG A;  2B67 A; 
#chains in the Genus database with same CATH homology
 1KQB A;  3BM1 A;  4BNB A;  2IFA A;  3M5K A;  1YKI A;  3X21 A;  3E10 A;  4TTC A;  2FRE A;  3GB5 A;  3GR3 A;  3EOF A;  3EO8 A;  4BN7 A;  3OF4 A;  2ISJ A;  1ZCH A;  1ICU A;  3H4O A;  5KO7 A;  1KQC A;  3QDL A;  1OOQ A;  4QLX A;  5HEI A;  3GFA A;  4BN6 A;  3G14 A;  3GH8 A;  1YWQ A;  1J6R A;  1OON A;  3BM2 A;  1OO5 A;  3KOQ A;  2R01 A;  3GBH A;  5J6C A;  1BKJ A;  2WZV A;  1V5Z A;  1YLR A;  4DN2 A;  1F5V A;  1V5Y A;  4XOM A;  2ISK A;  3E39 A;  3GE5 A;  3HZN A;  4QLY A;  1DS7 A;  2WZW A;  4EO3 A;  4XOQ A;  3BEM A;  1YLU A;  3HJ9 A;  3EK3 A;  1VFR A;  3K6H A;  2YMV A;  1ICV A;  3PXV A;  3GE6 A;  1ICR A;  1VKW A;  5KO8 A;  2HAY A;  2BKJ A;  2WQF A;  4BN9 A;  3TO0 A;  3EO7 A;  3TNZ A;  2I7H A;  3X22 A;  3N2S A;  1OO6 A;  4G8S A;  1IDT A;  5HDJ A;  5KRD A;  3GFD A;  1NEC A;  3HOI A;  2H0U A;  2ISL A;  4XOO A;  1NOX A;  1KQD A;  4TTB A;  3KWK A;  4URP A;  4BN8 A;  3GAG A;  2B67 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)

 
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