4I1KA

Crystal structure of vrn1 (residues 208-341)
Total Genus 27
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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
27
sequence length
118
structure length
118
Chain Sequence
TVTAEERERAINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAEKQWPVRCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRVN
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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 Arabidopsis B3 Domain Protein VERNALIZATION1 (VRN1) Is Involved in Processes Essential for Development, with Structural and Mutational Studies Revealing Its DNA-binding Surface.
pubmed doi rcsb
molecule tags Dna binding protein
source organism Arabidopsis thaliana
molecule keywords B3 domain-containing transcription factor VRN1
total genus 27
structure length 118
sequence length 118
chains with identical sequence B
ec nomenclature
pdb deposition date 2012-11-21

pfam database annotations

chain Pfam Accession Code Pfam Family Identifier Pfam Description
A PF02362 B3 B3 DNA binding domain
Image from the rcsb pdb (www.rcsb.org)
cath code
ClassArchitectureTopologyHomologyDomain
2.40.330.10 Mainly Beta Beta Barrel At1g16640 B3 domain DNA-binding pseudobarrel domain 4i1kA00
4LDVA 3HQFA 1YELA 4LDXA 1NA6A 4LDWA 4LDYA 4I1KA 4LDUA 1WIDA
chains in the Genus database with same CATH superfamily
4LDVA 3HQFA 1YELA 2C1LA 1NA6A 4LDWA 4LDXA 3ZI5A 1N0GA 4LDYA 1N0EA 4I1KA 4LDUA 1N0FA 1WIDA
chains in the Genus database with same CATH topology
4LDVA 3HQFA 1YELA 4LDXA 1NA6A 4LDWA 4LDYA 4I1KA 4LDUA 1WIDA
chains in the Genus database with same CATH homology


 
#chains in the Genus database with same CATH superfamily
 4LDV A;  3HQF A;  1YEL A;  4LDX A;  1NA6 A;  4LDW A;  4LDY A;  4I1K A;  4LDU A;  1WID A; 
#chains in the Genus database with same CATH topology
 4LDV A;  3HQF A;  1YEL A;  2C1L A;  1NA6 A;  4LDW A;  4LDX A;  3ZI5 A;  1N0G A;  4LDY A;  1N0E A;  4I1K A;  4LDU A;  1N0F A;  1WID A; 
#chains in the Genus database with same CATH homology
 4LDV A;  3HQF A;  1YEL A;  4LDX A;  1NA6 A;  4LDW A;  4LDY A;  4I1K A;  4LDU A;  1WID 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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