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
source organism Pseudomonas aeruginosa
molecule tags Transcription/dna
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
2BNZA 2BA3A 4HV0A 1ARQA 4FXEA 2K6LA 2KELA 2K1OA 3GXQA 2K9IA 2BJ3A 3QOQA 3FT7A 2BJ8A 2CPGA 1U9PA 2WVEA 3VW4A 1PARA 2CADA 2K29A 2WVDA 1ARRA 2BJ9A 2WVBA 1MYKA 2WVFA 3VEBA 2HZAA 2GPEA 3LGHA 2BSQE 2H1OE 4D8JA 2K5JA 2BJ7A 1IRQA 1NLAA 2BJ1A 3H87C 4ME7E 1BDTA 2CA9A 1MNTA 2JXIA 1X93A 2AY0A 3OD2A 1BAZA 1EA4A 2CAXA 3VEAA 1B28A 1Q5VA 2HZVA 2CAJA 2WVCA 1QTGA 2JXHA 1BDVA 2BNWA 1B01A 2JXGA 1MYLA 2RBFA 3FMTA 1P94A
chains in the Genus database with same CATH superfamily
2BA3A 1ARQA 1SH2A 3GXQA 2K9IA 3FT7A 2BJ8A 3IR7A 3UQSA 3QIDA 2B43A 2KOEA 1OHNA 2CKWA 4AAIA 2H3AA 3SFGA 1SH0A 1IRQA 4ME7E 2CA9A 2JXIA 3OD2A 4LQ3A 1B28A 1Q5VA 2WVCA 1B01A 4QPXA 2JXGA 2RBFA 1EA4A 2K1OA 2BJ3A 2CPGA 3SFUA 2KKEA 1OG7A 2ADLA 2AN7A 2WVDA 1ARRA 2WVBA 3H5YA 2HZAA 2H1OE 3H87C 1BDTA 4LQ9A 3VEAA 3BSNA 2Q2KA 4NRTA 1MYLA 3FMTA 2BNZA 2K6LA 2KELA 1U9PA 4O4RA 3VW4A 3NO7A 2CADA 2K29A 3NAHA 4MJWA 1MYKA 2BJ1A 2A2BA 1BAZA 2CAXA 1QTGA 1SIWA 1BDVA 2BNWA 1P94A 4HV0A 4FXEA 3QOQA 1Q16A 2WVEA 4NRUA 2WK4A 3NNEA 3NAIA 2UUWA 3LJPA 1PARA 3H5XA 2BJ9A 2WVFA 3UPFA 3VEBA 2GPEA 3LGHA 2BSQE 2JBVA 4D8JA 2K5JA 2BJ7A 1NLAA 3G5OA 1MNTA 1X93A 2AY0A 2UUTA 1SH3A 2HZVA 4LRVA 2CAJA 2JXHA 3BSOA 3UR0A
chains in the Genus database with same CATH topology
2BNZA 2BA3A 4HV0A 1ARQA 4FXEA 2K6LA 2KELA 2K1OA 3GXQA 2K9IA 2BJ3A 3QOQA 3FT7A 2BJ8A 2CPGA 1U9PA 2WVEA 3VW4A 1PARA 2CADA 2K29A 2WVDA 1ARRA 2BJ9A 2WVBA 1MYKA 2WVFA 3VEBA 2HZAA 2GPEA 3LGHA 2BSQE 2H1OE 4D8JA 2K5JA 2BJ7A 1IRQA 1NLAA 2BJ1A 3H87C 4ME7E 1BDTA 2CA9A 1MNTA 2JXIA 1X93A 2AY0A 3OD2A 1BAZA 1EA4A 2CAXA 3VEAA 1B28A 1Q5VA 2HZVA 2CAJA 2WVCA 1QTGA 2JXHA 1BDVA 2BNWA 1B01A 2JXGA 1MYLA 2RBFA 3FMTA 1P94A
chains in the Genus database with same CATH homology


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