3H5F

Switching the Chirality of the Metal Environment Alters the Coordination Mode in Designed Peptides.

• PDB DOI: https://doi.org/10.2210/pdb3H5F/pdb

• Classification: DE NOVO PROTEIN
• Mutation(s): No 


• Deposited: 2009-04-22 Released: 2009-07-14 
• Deposition Author(s): Peacock, A.F.A., Stuckey, J.A., Pecoraro, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.255 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 

Literature

Switching the Chirality of the Metal Environment Alters the Coordination Mode in Designed Peptides.

Peacock, A.F., Stuckey, J.A., Pecoraro, V.L.

(2009) Angew Chem Int Ed Engl 48: 7371-7374

• PubMed: 19579245 
• DOI: https://doi.org/10.1002/anie.200902166
• Primary Citation of Related Structures:  
  3H5F, 3H5G


• PubMed Abstract: 
  

  The effects of switching the chirality of a single layer of amino acids in a three stranded coiled coil has been investigated. X-ray crystallography reveals that this modification is well tolerated and does not alter the designed structure. In contrast, spectroscopic studies of cadmium binding to both the L- and D- enantiomers of the penicillamine, provide evidence that this switch dramatically alters the metal binding capability, the resulting coordination environment and the position of binding.

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Organizational Affiliation: 

Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.49 kDa 
• Atom Count: 822 
• Modelled Residue Count: 93 
• Deposited Residue Count: 93 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COIL SER L16L-Pen	A, B, C	31	N/A	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], I [auth C], J [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	K [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	D [auth A], G [auth B], H [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LE1	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 S		VAL

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.86 Å
• R-Value Free: 0.255 
• R-Value Work: 0.199 
• R-Value Observed: 0.202 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.827	α = 90
b = 29.244	β = 118.8
c = 44.46	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Peacock, A.F.A., Stuckey, J.A., Pecoraro, V.L.

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2022-05-04
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection