Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.17 kDa 
• Atom Count: 556 
• Modelled Residue Count: 64 
• Deposited Residue Count: 64 
• Unique protein chains: 1

1YPB

DIRECT OBSERVATION OF BETTER HYDRATION AT THE N-TERMINUS OF AN ALPHA-HELIX WITH GLYCINE RATHER THAN ALANINE AS N-CAP

• PDB DOI: 10.2210/pdb1YPB/pdb

• Classification: PROTEINASE INHIBITOR(CHYMOTRYPSIN)
• Organism(s): Hordeum vulgare
• Mutation(s): No 


• Deposited: 1993-01-10 Released: 1994-01-31 
• Deposition Author(s): Harpaz, Y., Elmasry, N., Fersht, A.R., Henrick, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.174 

Literature

Direct observation of better hydration at the N terminus of an alpha-helix with glycine rather than alanine as the N-cap residue.

Harpaz, Y., Elmasry, N., Fersht, A.R., Henrick, K.

(1994) Proc Natl Acad Sci U S A 91: 311-315

• PubMed: 8278384 
• DOI: 10.1073/pnas.91.1.311
• Primary Citation of Related Structures:  
  1YPA, 1YPB, 1YPC


• PubMed Abstract: 
  

The structural basis for the stability of N termini of helices has been analyzed by thermodynamic and crystallographic studies of three suitably engineered mutants of the barley chymotrypsin inhibitor 2 with Ser, Gly, or Ala at the N-cap position (residue 31). Each mutant has a well-organized shell of hydration of the terminal NH groups of the helix. The three structures are virtually superimposable (rms separations for all atoms, including the common water molecules, are 0.15-0.17 A) and show neither changes in conformation at the site of substitution nor changes in the crystal packing. The only changes on going from Ser-31 to Ala-31 to Gly-31 are in the position of a water molecule (Wat-116). This is bound to the Ser-O gamma atom in the Ser-31 structure but is in a weak hydrogen bonding position with the NH of residue 34 (O ... N = 3.28 A) in the Ala-31 mutant, partly replacing the strong Ser-31-O gamma ... N34 hydrogen bond (O ... N = 2.65 A). The corresponding water molecule completely replaces the Ser hydroxyl hydrogen bond to N34 on mutation to Gly (2.74 A). The only other change between the three structures is an additional water molecule in the Ala-31 structure (Wat-150) that partly compensates for the weak Wat-116 ... N34 hydrogen bond. Perturbation of solvation by the side chain of Ala is consistent with earlier hypotheses on the importance of exposure of the termini of helices to the aqueous solvent.

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Organizational Affiliation: 

Centre for Protein Engineering, Medical Research Council Centre, Cambridge, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHYMOTRYPSIN INHIBITOR 2	A [auth I]	64	Hordeum vulgare	Mutation(s): 0
UniProt
Find proteins for P01053 (Hordeum vulgare) Explore P01053  Go to UniProtKB:  P01053

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Observed: 0.174 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.16	α = 90
b = 33.65	β = 90
c = 55.99	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-01-10 
• Released Date: 1994-01-31 
Deposition Author(s): Harpaz, Y., Elmasry, N., Fersht, A.R., Henrick, K.

Revision History  

• Version 1.0: 1994-01-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other