› 8z1y

Electron Microscopy
2.73Å resolution

Cryo-EM structure of Escherichia coli DppABCDF in the pre-catalytic state

Released:
DOI: 10.2210/pdb8z1y/pdb
PDB entry 8z1y coloured by chain, front view.
PDB entry 8z1y coloured by chain, side view.
PDB entry 8z1y coloured by chain, top view.
Source organism: Escherichia coli K-12
Entry authors: Li P, Huang Y
Related structures: EMD-39740

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + a dipeptide-[dipeptide-binding protein](Side 1) = ADP + phosphate + a dipeptide(Side 2) + [dipeptide-binding protein](Side 1)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-284556 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Dipeptide transport system permease protein DppB Chain: A
Molecule details ›
Chain: A
Length: 339 amino acids
Theoretical weight: 37.53 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AEF8 (Residues: 1-339; Coverage: 100%)
Gene names: JW3512, b3543, dppB
Sequence domains:
Dipeptide transport system permease protein DppC Chain: B
Molecule details ›
Chain: B
Length: 300 amino acids
Theoretical weight: 32.33 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AEG1 (Residues: 1-300; Coverage: 100%)
Gene names: JW3511, b3542, dppC
Sequence domains:
Dipeptide transport ATP-binding protein DppD Chain: C
Dipeptide transport ATP-binding protein DppF Chain: D
Dipeptide-binding protein Chain: F

Ligands and Environments

2 bound ligands:
Ligand AGS 2 x AGS
Ligand SF4 2 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.73Å
Relevant EMDB volumes: EMD-39740
Expression system: Escherichia coli

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