1AA4

SPECIFICITY OF LIGAND BINDING IN A BURIED POLAR CAVITY OF CYTOCHROME C PEROXIDASE

• PDB DOI: https://doi.org/10.2210/pdb1AA4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1997-01-22 Released: 1997-07-23 
• Deposition Author(s): Musah, R.A., Fitzgerald, M.M., Mcree, D.E., Goodin, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.189 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

A ligand-gated, hinged loop rearrangement opens a channel to a buried artificial protein cavity.

Fitzgerald, M.M., Musah, R.A., McRee, D.E., Goodin, D.B.

(1996) Nat Struct Biol 3: 626-631

• PubMed: 8673607 
• DOI: https://doi.org/10.1038/nsb0796-626
• Primary Citation of Related Structures:  
  1AA4, 1AES, 1AET, 1AEU, 1CCI, 1RYC


• PubMed Abstract: 
  

  Conformational changes that gate the access of substrates or ligands to an active site are important features of enzyme function. In this report, we describe an unusual example of a structural rearrangement near a buried artificial cavity in cytochrome c peroxidase that occurs on binding protonated benzimidazole. A hinged main-chain rotation at two residues (Pro 190 and Asn 195) results in a surface loop rearrangement that opens a large solvent-accessible channel for the entry of ligands to an otherwise inaccessible binding site. The trapping of this alternate conformational state provides a unique view of the extent to which protein dynamics can allow small molecule penetration into buried protein cavities.

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Organizational Affiliation: 

Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.07 kDa 
• Atom Count: 2,488 
• Modelled Residue Count: 291 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME C PEROXIDASE	A	294	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: CCP EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00431  Go to UniProtKB:  P00431

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Work: 0.189 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108	α = 90
b = 77.3	β = 90
c = 51.8	γ = 90

Software Package:

Software Name	Purpose
XTALVIEW	refinement
X-PLOR	refinement
XENGEN	data reduction
XENGEN	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-07-23 
Deposition Author(s): Musah, R.A., Fitzgerald, M.M., Mcree, D.E., Goodin, D.B.

Revision History  

• Version 1.0: 1997-07-23
  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: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-02
  Changes: Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection