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DdmD monomer in complex with ssDNA

Electron Microscopy
2.99Å resolution
PDB entry 8u0w coloured by chain, front view.
PDB entry 8u0w coloured by chain, side view.
PDB entry 8u0w coloured by chain, top view.
Source organisms:
Assembly composition:
hetero dimer (preferred)
Entry contents: 1 distinct polypeptide molecule
1 distinct DNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Helicase/UvrB N-terminal domain-containing protein and DNA
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Multimeric state: hetero dimer
Accessible surface area: 50114.83 Å2
Buried surface area: 2792.18 Å2
Dissociation area: 1,396.09 Å2
Dissociation energy (ΔGdiss): 18.79 kcal/mol
Dissociation entropy (TΔSdiss): 10.73 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-270047

Macromolecules

Helicase/UvrB N-terminal domain-containing protein
Chain: A
Length: 1220 amino acids
Theoretical weight: 140.01 KDa
Source organism: Vibrio cholerae
Expression system: Escherichia coli
UniProt:
  • Canonical: B9TSM3 (Residues: 1-1220; Coverage: 100%)
Gene name: VPI2_0019c
Helicase/UvrB N-terminal domain-containing protein in PDB entry 8u0w, assembly 1, front view.
Helicase/UvrB N-terminal domain-containing protein in PDB entry 8u0w, assembly 1, side view.
Helicase/UvrB N-terminal domain-containing protein in PDB entry 8u0w, assembly 1, top view.
PDBe-KB: UniProt Coverage View: B9TSM3  
112201002003004005006007008009001,0001,1001,200
 
5001000MFMYSVFTCRYWRYIMVRLIKHQQLLGEYCMNVSIEEFTHFDFQLVPEPSPLDLVITESLKNHIEVNGVKSGALLPLPFQTGIGKTYTALNFLLQQMLEQVRSELKEENTGKKSKRLLYYVTDSVDNVVSAKADLLKLIEKQTVKGEPRFTLEQQEYLKAQIVHLPNQSEQLLQCSDAVLNDVLIGFNLNAERDVQAEWSAISGLRRHASNPEVKISLNRQAGYFYRNLIDRLQKKQKGADRVLLSGSLLASVETLLPGEKIRNGSAHVAFLTTSKFLKGFHNTRSRYSPLRDLSGAVLIIDEIDKQNQVILSELCKQQAQDLIWAIRTLRANFRDHQLESSPRYDKIEDLFEPLRERLEEFGTNWNLAFAFNTEGANLNERPVRLFSDRSFTHVSSATHKLSLKSDFLRRKNLIFSDEKVEGSLIEKHGLLTRFVNEADVIYQWFLGTMRKAVFQYWENVRGLEIEVRENRSLEGTFQEAVQSLLTHFNLQEFESAVYESFDTRGLRQSAGGKANKLSSSKSYHHTGLKLVEVAHNQGTRDTVNCKASFLNTSPSGVLADMVDAGAVILGISATARADTVIHNFDFKYLNERLGNKLLSLSREQKQRVNNYYHSRRNYKDNGVVLTVKYLNSRDAFLDALLEEYKPEARSSHFILNHYLGIAESEQAFVRSWLSKLLASIKAFISSPDNRYMLSLLNRTLDTTRQNINDFIQFCCDKWAKEFNVKTKTFFGVNADWMRLVGYDEISKHLNTELGKVVVFSTYASMGAGKNPDYAVNLALEGESLISVADVTYSTQLRSDIDSIYLEKPTQLLLSDDYSHTANQLCQFHQILSLQENGELSPKSAENWCRQQLMGMSRERSLQQYHQTSDYQSAVRKYIEQAVGRAGRTSLKRKQILLFVDSGLKEILAEESRDPSLFSHEYVALVNKAKSAGKSIVEDRAVRRLFNLAQRNNKDGMLSIKALVHRLHNQPASKSDIQEWQDIRTQLLRYPTVAFQPERFNRLYLQSMTKGYYRYQGNLDGDPNSFEFFDRVPYGDMVSEEDCSLATLVQNQYVRPWFERKGFACSWQKEANVMTPIMFTNIYKGALGEQAVEAVLTAFDFTFEEVPNSIYERFDNRVIFAGIEQPIWLDSKYWKHEGNESSEGYSSKIALVEEEFGPSKFIYVNALGDTSKPIRYLNSCFVETSPQLAKVIEIPALIDDSNADTNRTAVQELIKWLHHS
UniProt
B9TSM3
Chains
Sequence conservation
Molecule details ›

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DNA chain C
Name: DNA (5'-D(P*TP*TP*AP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')
Representative chains: C
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.61 KDa
DNA (5'-D(P*TP*TP*AP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') in PDB entry 8u0w, assembly 1, front view.
DNA (5'-D(P*TP*TP*AP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') in PDB entry 8u0w, assembly 1, side view.
DNA (5'-D(P*TP*TP*AP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') in PDB entry 8u0w, assembly 1, top view.
112123456789101112
 
510TTATTTTTTTTT
Chains
Chain B (auth C)
Interaction interfaces
Molecule details ›

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