1BDV | Genus

Total Genus 16

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	16
sequence length	46
structure length	46
Chain Sequence	MPQVNLRWPREVLDLVRKVAEENGRSVNSEIYQRVMESFKKEGRIG

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

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reading 46 atoms

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After clicking on a point (x,y) in the genus matrix above, a subchain from x to y is shown in color.

Genus data interpretation

Chord Diagram

molecule tags	Gene regulation/dna
source organism	Enterobacteria phage p22
publication title	Origins of DNA-binding specificity: role of protein contacts with the DNA backbone. pubmed doi rcsb
molecule keywords	DNA (5'-D(TPAPTPAPGPTPAPGPAPGPTPGPCPTPTPCP*T
total genus	16
structure length	46
sequence length	46
chains with identical sequence	B, C, D
ec nomenclature
pdb deposition date	1998-05-11

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	Class	Architecture	Topology	Homology	Domain
1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	1bdvA00

3VEBA 2BJ9A 2KELA 1P94A 1BDVA 3LGHA 1BDTA 1B28A 2BNWA 2CPGA 2WVBA 2CA9A 3H87C 1U9PA 1EA4A 1BAZA 2WVCA 2H1OE 2K9IA 4FXEA 2JXIA 1Q5VA 2K1OA 1MYKA 2BNZA 2AY0A 2JXGA 1MNTA 2K5JA 3GXQA 2BJ3A 3VEAA 2BJ1A 2BA3A 2K29A 4ME7E 1QTGA 2K6LA 1MYLA 2BSQE 1IRQA 3FMTA 2RBFA 2CAXA 2BJ8A 1X93A 1ARRA 2CADA 2WVDA 3VW4A 4HV0A 1ARQA 2HZAA 3FT7A 4D8JA 2BJ7A 2CAJA 3QOQA 2GPEA 1NLAA 1B01A 2WVFA 2JXHA 2HZVA 3OD2A 2WVEA 1PARA
chains in the Genus database with same CATH superfamily

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

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

Total Genus

sequence length

structure length

Chain Sequence

Structure visualization

Chord Diagram

connected with : NaN

pfam database annotations