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PDBsum entry 1b3h
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Peptide binding protein PDB id
1b3h

 

 

 

 

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Contents
Protein chain
517 a.a. *
Ligands
LYS-ALC-LYS
Metals
_U1 ×8
Waters ×249
* Residue conservation analysis
PDB id:
1b3h
Name: Peptide binding protein
Title: Oligo-peptide binding protein complexed with lysyl-cyclohexylalanyl- lysine
Structure: Periplasmic oligopeptide-binding protein. Chain: a. Synonym: oppa. Engineered: yes. Lys-alc-lys peptide. Chain: b. Synonym: lys-alc-lys. Engineered: yes
Source: Salmonella typhimurium. Organism_taxid: 602. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.190     R-free:   0.240
Authors: T.G.Davies,J.R.H.Tame
Key ref: T.G.Davies et al. (1999). Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci, 8, 1432-1444. PubMed id: 10422831 DOI: 10.1110/ps.8.7.1432
Date:
11-Nov-98     Release date:   18-Nov-98    
PROCHECK
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 Headers
 References

Protein chain
P06202  (OPPA_SALTY) -  Periplasmic oligopeptide-binding protein OppA from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Seq:
Struc: 		 
Seq:
Struc: 		543 a.a.
517 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1110/ps.8.7.1432 Protein Sci 8:1432-1444 (1999)
PubMed id: 10422831  
 
 
Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.
T.G.Davies, R.E.Hubbard, J.R.Tame.
 
  ABSTRACT  
 
The oligopeptide-binding protein OppA provides a useful model system for studying the physical chemistry underlying noncovalent interactions since it binds a variety of readily synthesized ligands. We have studied the binding of eight closely related tripeptides of the type Lysine-X-Lysine, where X is an abnormal amino acid, by isothermal titration calorimetry (ITC) and X-ray crystallography. The tripeptides fall into three series of ligands, which have been designed to examine the effects of small changes to the central side chain. Three ligands have a primary amine as the second side chain, two have a straight alkane chain, and three have ring systems. The results have revealed a definite preference for the binding of hydrophobic residues over the positively charged side chains, the latter binding only weakly due to unfavorable enthalpic effects. Within the series of positively charged groups, a point of lowest affinity has been identified and this is proposed to arise from unfavorable electrostatic interactions in the pocket, including the disruption of a key salt bridge. Marked entropy-enthalpy compensation is found across the series, and some of the difficulties in designing tightly binding ligands have been highlighted.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20582607 F.Tian, L.Yang, F.Lv, X.Luo, and Y.Pan (2011).
Why OppA protein can bind sequence-independent peptides? A combination of QM/MM, PB/SA, and structure-based QSAR analyses.
  Amino Acids, 40, 493-503.  
  21469159 S.Y.Lu, Y.J.Jiang, J.Lv, J.W.Zou, and T.X.Wu (2011).
Role of bridging water molecules in GSK3β-inhibitor complexes: insights from QM/MM, MD, and molecular docking studies.
  J Comput Chem, 32, 1907-1918.  
20345171 C.Bissantz, B.Kuhn, and M.Stahl (2010).
A medicinal chemist's guide to molecular interactions.
  J Med Chem, 53, 5061-5084.  
19559587 A.Taneoka, A.Sakaguchi-Mikami, T.Yamazaki, W.Tsugawa, and K.Sode (2009).
The construction of a glucose-sensing luciferase.
  Biosens Bioelectron, 25, 76-81.  
18414800 A.Sakaguchi-Mikami, A.Taneoka, R.Yamoto, S.Ferri, and K.Sode (2008).
Engineering of ligand specificity of periplasmic binding protein for glucose sensing.
  Biotechnol Lett, 30, 1453-1460.  
17015009 A.Sakaguchi, S.Ferri, W.Tsugawa, and K.Sode (2007).
Novel fluorescent sensing system for alpha-fructosyl amino acids based on engineered fructosyl amino acid binding protein.
  Biosens Bioelectron, 22, 1933-1938.  
15281134 D.B.Sherman, S.Zhang, J.B.Pitner, and A.Tropsha (2004).
Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.
  Proteins, 56, 828-838.  
14993672 G.Kontopidis, P.Taylor, and M.D.Walkinshaw (2004).
Enzymatic and structural characterization of non-peptide ligand-cyclophilin complexes.
  Acta Crystallogr D Biol Crystallogr, 60, 479-485.
PDB codes: 1w8l 1w8m 1w8v
12538891 A.M.Hays, H.B.Gray, and D.B.Goodin (2003).
Trapping of peptide-based surrogates in an artificially created channel of cytochrome c peroxidase.
  Protein Sci, 12, 278-287.  
12391580 K.Benkestock, P.O.Edlund, and J.Roeraade (2002).
On-line microdialysis for enhanced resolution and sensitivity during electrospray mass spectrometry of non-covalent complexes and competitive binding studies.
  Rapid Commun Mass Spectrom, 16, 2054-2059.  
10899119 F.C.Lanfermeijer, F.J.Detmers, W.N.Konings, and B.Poolman (2000).
On the binding mechanism of the peptide receptor of the oligopeptide transport system of Lactococcus lactis.
  EMBO J, 19, 3649-3656.  
11050157 F.J.Detmers, F.C.Lanfermeijer, R.Abele, R.W.Jack, R.Tampe, W.N.Konings, and B.Poolman (2000).
Combinatorial peptide libraries reveal the ligand-binding mechanism of the oligopeptide receptor OppA of Lactococcus lactis.
  Proc Natl Acad Sci U S A, 97, 12487-12492.  
10826972 H.J.Böhm, and M.Stahl (2000).
Structure-based library design: molecular modelling merges with combinatorial chemistry.
  Curr Opin Chem Biol, 4, 283-286.  
10771422 J.Habash, J.Raftery, R.Nuttall, H.J.Price, C.Wilkinson, A.J.Kalb, and J.R.Helliwell (2000).
Direct determination of the positions of the deuterium atoms of the bound water in -concanavalin A by neutron Laue crystallography.
  Acta Crystallogr D Biol Crystallogr, 56, 541-550.
PDB codes: 1c57 1qny
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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