1DPP

DIPEPTIDE BINDING PROTEIN COMPLEX WITH GLYCYL-L-LEUCINE

• PDB DOI: https://doi.org/10.2210/pdb1DPP/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1995-08-11 Released: 1995-12-07 
• Deposition Author(s): Dunten, P., Mowbray, S.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

Crystal structure of the dipeptide binding protein from Escherichia coli involved in active transport and chemotaxis.

Dunten, P., Mowbray, S.L.

(1995) Protein Sci 4: 2327-2334

• PubMed: 8563629 
• DOI: https://doi.org/10.1002/pro.5560041110
• Primary Citation of Related Structures:  
  1DPP


• PubMed Abstract: 
  

  The Escherichia coli periplasmic dipeptide binding protein functions in both peptide transport and taxis toward peptides. The structure of the dipeptide binding protein in complex with Gly-Leu (glycyl-L-leucine) has been determined at 3.2 A resolution. The binding site for dipeptides is designed to recognize the ligand's backbone while providing space to accommodate a variety of side chains. Some repositioning of protein side chains lining the binding site must occur when the dipeptide's second residue is larger than leucine. The protein's fold is very similar to that of the Salmonella typhimurium oligopeptide binding protein, and a comparison of the structures reveals the structural basis for the dipeptide binding protein's preference for shorter peptides.

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Organizational Affiliation: 

Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 230.73 kDa 
• Atom Count: 16,244 
• Modelled Residue Count: 2,028 
• Deposited Residue Count: 2,028 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPEPTIDE BINDING PROTEIN	A, B [auth C], C [auth E], D [auth G]	507	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P23847 (Escherichia coli (strain K12)) Explore P23847  Go to UniProtKB:  P23847

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LEU	F [auth A], H [auth C], J [auth E], L [auth G]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
GLY	E [auth A], G [auth C], I [auth E], K [auth G]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.57	α = 90
b = 182.57	β = 90
c = 211.88	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-12-07 
Deposition Author(s): Dunten, P., Mowbray, S.L.

Revision History  

• Version 1.0: 1995-12-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary