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Wheat dwarf virus rep domain complexed with a single-stranded DNA 8- mer comprising the cleavage site

Analyse Wheat dwarf virus rep domain complexed with a single-stranded DNA 8- mer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6WE1
Type
protein + DNA
Length
245 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Replication-associated protein; DNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3')
EC
3.1.21.-
UniProt
A0A0F6N3D1
Ligands
MN

Structure

x-ray diffraction · 3 distinct chains · 24% helix, 41% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AReplication-associated protein (EC 3.1.21.-)protein11624% helix, 41% strandA0A0F6N3D1
C, FDNA (5'-D(*AP*AP*TP*AP*TP*TP*AP*C)-3')dna8——
DReplication-associated protein (EC 3.1.21.-)protein11325% helix, 41% strandA0A0F6N3D1

Ligands and binding sites

  • MN · Manganese (II) ion · metal · 3 copies · chains A, C, F, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

5 interfaces between chains.

  • A–C · 785 Ų buried · 19 hydrogen bonds · protein-nucleic
  • F–D · 749 Ų buried · 19 hydrogen bonds · protein-nucleic
  • C–F · 281 Ų buried · 12 hydrogen bonds · nucleic-nucleic
  • A–F · 150 Ų buried · 1 hydrogen bond · protein-nucleic
  • C–D · 143 Ų buried · 2 hydrogen bonds · protein-nucleic

Compared structures

  • 6WE1 · Wheat dwarf virus Rep domain complexed with a single-stranded DNA 8-mer comprising the… · the same entry in another collection · chain A against A, TM-score 1.00

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