1CCI | pdb_00001cci

HOW FLEXIBLE ARE PROTEINS? TRAPPING OF A FLEXIBLE LOOP

• PDB DOI: https://doi.org/10.2210/pdb1CCI/pdb

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


• Deposited: 1996-12-18 Released: 1997-07-07 
• Deposition Author(s): Cao, Y., Musah, R.A., Wilcox, S.K., Goodin, D.B., Mcree, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work: 
  0.371 (DCC) 

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 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: 34.21 kDa 
• Atom Count: 2,490 
• Modeled 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): 3  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
DMI	B [auth A]	2,3-DIMETHYLIMIDAZOLIUM ION C5 H9 N2 GIWQSPITLQVMSG-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.371 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.72	α = 90
b = 76.63	β = 90
c = 51.68	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-07-07 
Deposition Author(s): Cao, Y., Musah, R.A., Wilcox, S.K., Goodin, D.B., Mcree, D.E.

Revision History  

• Version 1.0: 1997-07-07
  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: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-09
  Changes: Refinement description
• Version 1.5: 2024-05-22
  Changes: Data collection