3QOQA

Crystal structure of the transcription factor amrz in complex with the 18 base pair amrz1 binding site
Total Genus 12
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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
12
sequence length
50
structure length
50
Chain Sequence
TYSSRTADKFVVRLPEGMREQIAEVARSHHRSMNSEIIARLEQSLLQEGA
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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 The Transcription Factor AmrZ Utilizes Multiple DNA Binding Modes to Recognize Activator and Repressor Sequences of Pseudomonas aeruginosa Virulence Genes.
pubmed doi rcsb
molecule tags Transcription/dna
source organism Pseudomonas aeruginosa
molecule keywords Alginate and motility regulator Z
total genus 12
structure length 50
sequence length 50
chains with identical sequence B, C, D
ec nomenclature
pdb deposition date 2011-02-10

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF03869 Arc Arc-like DNA binding domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
1.10.1220.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant Met repressor-like 3qoqA00
2HZVA 2K5JA 2AY0A 3QOQA 2H1OE 1PARA 1EA4A 3FT7A 2WVDA 2BJ9A 1MYLA 3H87C 2BNZA 4ME7E 3VW4A 2JXIA 1BAZA 2WVBA 2JXGA 2KELA 2CPGA 2GPEA 2BJ1A 2K6LA 4D8JA 1IRQA 2CAXA 2CAJA 2BA3A 3VEAA 1ARQA 3VEBA 1U9PA 1MYKA 1Q5VA 3LGHA 3FMTA 1P94A 3OD2A 2BNWA 2WVCA 1B28A 1MNTA 2CA9A 2K1OA 2CADA 2WVFA 2K29A 2RBFA 3GXQA 1BDVA 2BJ7A 1ARRA 1BDTA 2WVEA 1NLAA 2BJ3A 4FXEA 2JXHA 4HV0A 1X93A 2BJ8A 2BSQE 1QTGA 2HZAA 1B01A 2K9IA
chains in the Genus database with same CATH superfamily
3QOQA 2H1OE 3IR7A 2AN7A 4ME7E 3VW4A 4O4RA 2JXGA 2CPGA 2GPEA 2CAXA 3NAIA 2CAJA 1Q16A 1ARQA 1SH2A 1B28A 2K1OA 3NAHA 3SFGA 2WVFA 2RBFA 3G5OA 3QIDA 2WVEA 4FXEA 2BJ3A 2JXHA 3UQSA 2CA9A 2ADLA 3NO7A 2AY0A 3FT7A 2BJ9A 2UUTA 3H87C 4LRVA 1OHNA 4NRUA 4D8JA 4LQ3A 1OG7A 2UUWA 2Q2KA 3VEBA 1MYKA 4AAIA 3FMTA 1P94A 3OD2A 2WVCA 2B43A 3H5YA 2A2BA 2BJ7A 1ARRA 3LJPA 1BDTA 2HZAA 1B01A 2HZVA 2K5JA 1PARA 2JBVA 3BSNA 2KKEA 1BAZA 2KELA 2BJ1A 2CKWA 3BSOA 3SFUA 2BA3A 3VEAA 3LGHA 2KOEA 2H3AA 2CADA 4QPXA 4LQ9A 2K29A 3GXQA 1BDVA 4MJWA 1X93A 1QTGA 2K9IA 1SIWA 1EA4A 2WVDA 1MYLA 2BNZA 2JXIA 2WVBA 2K6LA 3UPFA 1IRQA 3H5XA 4NRTA 1U9PA 1Q5VA 2BNWA 1MNTA 1SH0A 3NNEA 1SH3A 3UR0A 1NLAA 4HV0A 2BJ8A 2BSQE 2WK4A
chains in the Genus database with same CATH topology
2HZVA 2K5JA 2AY0A 3QOQA 2H1OE 1PARA 1EA4A 3FT7A 2WVDA 2BJ9A 1MYLA 3H87C 2BNZA 4ME7E 3VW4A 2JXIA 1BAZA 2WVBA 2JXGA 2KELA 2CPGA 2GPEA 2BJ1A 2K6LA 4D8JA 1IRQA 2CAXA 2CAJA 2BA3A 3VEAA 1ARQA 3VEBA 1U9PA 1MYKA 1Q5VA 3LGHA 3FMTA 1P94A 3OD2A 2BNWA 2WVCA 1B28A 1MNTA 2CA9A 2K1OA 2CADA 2WVFA 2K29A 2RBFA 3GXQA 1BDVA 2BJ7A 1ARRA 1BDTA 2WVEA 1NLAA 2BJ3A 4FXEA 2JXHA 4HV0A 1X93A 2BJ8A 2BSQE 1QTGA 2HZAA 1B01A 2K9IA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 2HZV A;  2K5J A;  2AY0 A;  3QOQ A;  2H1O E;  1PAR A;  1EA4 A;  3FT7 A;  2WVD A;  2BJ9 A;  1MYL A;  3H87 C;  2BNZ A;  4ME7 E;  3VW4 A;  2JXI A;  1BAZ A;  2WVB A;  2JXG A;  2KEL A;  2CPG A;  2GPE A;  2BJ1 A;  2K6L A;  4D8J A;  1IRQ A;  2CAX A;  2CAJ A;  2BA3 A;  3VEA A;  1ARQ A;  3VEB A;  1U9P A;  1MYK A;  1Q5V A;  3LGH A;  3FMT A;  1P94 A;  3OD2 A;  2BNW A;  2WVC A;  1B28 A;  1MNT A;  2CA9 A;  2K1O A;  2CAD A;  2WVF A;  2K29 A;  2RBF A;  3GXQ A;  1BDV A;  2BJ7 A;  1ARR A;  1BDT A;  2WVE A;  1NLA A;  2BJ3 A;  4FXE A;  2JXH A;  4HV0 A;  1X93 A;  2BJ8 A;  2BSQ E;  1QTG A;  2HZA A;  1B01 A;  2K9I A; 
#chains in the Genus database with same CATH topology
 3QOQ A;  2H1O E;  3IR7 A;  2AN7 A;  4ME7 E;  3VW4 A;  4O4R A;  2JXG A;  2CPG A;  2GPE A;  2CAX A;  3NAI A;  2CAJ A;  1Q16 A;  1ARQ A;  1SH2 A;  1B28 A;  2K1O A;  3NAH A;  3SFG A;  2WVF A;  2RBF A;  3G5O A;  3QID A;  2WVE A;  4FXE A;  2BJ3 A;  2JXH A;  3UQS A;  2CA9 A;  2ADL A;  3NO7 A;  2AY0 A;  3FT7 A;  2BJ9 A;  2UUT A;  3H87 C;  4LRV A;  1OHN A;  4NRU A;  4D8J A;  4LQ3 A;  1OG7 A;  2UUW A;  2Q2K A;  3VEB A;  1MYK A;  4AAI A;  3FMT A;  1P94 A;  3OD2 A;  2WVC A;  2B43 A;  3H5Y A;  2A2B A;  2BJ7 A;  1ARR A;  3LJP A;  1BDT A;  2HZA A;  1B01 A;  2HZV A;  2K5J A;  1PAR A;  2JBV A;  3BSN A;  2KKE A;  1BAZ A;  2KEL A;  2BJ1 A;  2CKW A;  3BSO A;  3SFU A;  2BA3 A;  3VEA A;  3LGH A;  2KOE A;  2H3A A;  2CAD A;  4QPX A;  4LQ9 A;  2K29 A;  3GXQ A;  1BDV A;  4MJW A;  1X93 A;  1QTG A;  2K9I A;  1SIW A;  1EA4 A;  2WVD A;  1MYL A;  2BNZ A;  2JXI A;  2WVB A;  2K6L A;  3UPF A;  1IRQ A;  3H5X A;  4NRT A;  1U9P A;  1Q5V A;  2BNW A;  1MNT A;  1SH0 A;  3NNE A;  1SH3 A;  3UR0 A;  1NLA A;  4HV0 A;  2BJ8 A;  2BSQ E;  2WK4 A; 
#chains in the Genus database with same CATH homology
 2HZV A;  2K5J A;  2AY0 A;  3QOQ A;  2H1O E;  1PAR A;  1EA4 A;  3FT7 A;  2WVD A;  2BJ9 A;  1MYL A;  3H87 C;  2BNZ A;  4ME7 E;  3VW4 A;  2JXI A;  1BAZ A;  2WVB A;  2JXG A;  2KEL A;  2CPG A;  2GPE A;  2BJ1 A;  2K6L A;  4D8J A;  1IRQ A;  2CAX A;  2CAJ A;  2BA3 A;  3VEA A;  1ARQ A;  3VEB A;  1U9P A;  1MYK A;  1Q5V A;  3LGH A;  3FMT A;  1P94 A;  3OD2 A;  2BNW A;  2WVC A;  1B28 A;  1MNT A;  2CA9 A;  2K1O A;  2CAD A;  2WVF A;  2K29 A;  2RBF A;  3GXQ A;  1BDV A;  2BJ7 A;  1ARR A;  1BDT A;  2WVE A;  1NLA A;  2BJ3 A;  4FXE A;  2JXH A;  4HV0 A;  1X93 A;  2BJ8 A;  2BSQ E;  1QTG A;  2HZA A;  1B01 A;  2K9I A; 
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similar chains in the Genus database (?% sequence similarity)
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#similar chains in the Genus database (?% sequence similarity)
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#similar chains, but unknotted
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