Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 12.67 kDa 
• Atom Count: 891 
• Modelled Residue Count: 108 
• Deposited Residue Count: 108 
• Unique protein chains: 1

1FHB

THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE CYANIDE ADDUCT OF A MET80ALA VARIANT OF SACCHAROMYCES CEREVISIAE ISO-1-CYTOCHROME C. IDENTIFICATION OF LIGAND-RESIDUE INTERACTIONS IN THE DISTAL HEME CAVITY

• PDB DOI: 10.2210/pdb1FHB/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1995-06-16 Released: 1995-09-15 
• Deposition Author(s): Banci, L., Bertini, I., Bren, K.L., Gray, H.B., Sompornpisut, P., Turano, P.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 17 

Literature

Three-Dimensional Solution Structure of the Cyanide Adduct of a met80Ala Variant of Saccharomyces Cerevisiae Iso-1-Cytochrome C. Identification of Ligand-Residue Interactions in the Distal Heme Cavity

Banci, L., Bertini, I., Bren, K.L., Gray, H.B., Sompornpisut, P., Turano, P.

(1995) Biochemistry 34: 11385-11398

• PubMed: 7547866 
• DOI: 10.1021/bi00036a011
• Primary Citation of Related Structures:  
  1FHB


• PubMed Abstract: 
  

The 1H NMR spectrum of the the cyanide adduct of a triply mutated Saccharomyces cerevisiae iso-1-cytochrome c (His39Gln/Met80Ala/Cys102Ser) in the oxidized form has been assigned through 1D NOE and 2D COSY, TOCSY, NOESY, and NOE-NOESY experiments; 562 protons out of a total of 683 have been assigned. The solution structure, the first of a paramagnetic heme protein, was determined using 1426 meaningful NOE constraints out of a total of 1842 measured NOEs. The RMSD values at the stage of restrained energy minimization of 17 structures obtained from distance geometry calculations are 0.68 +/- 0.11 and 1.32 +/- 0.14 A for the backbone and all heavy atoms, respectively. The quality, in terms of RMSD, of the present structure is the same as that obtained for the solution structure of the diamagnetic horse heart ferrocytochrome c [Qi, P. X., et al. (1994) Biochemistry 33, 6408-6419]. The secondary structure elements and the overall folding in the variant are observed to be the same as those of the wild-type protein for which the X-ray structure is available. However, the replacement of the methionine axial ligand with an alanine residue creates a ligand-binding "distal cavity". The properties of the distal cavity seen in this solution structure are compared to those of other heme proteins.

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Related Citations: 

• Paramagnetic 1H NMR Spectroscopy of the Cyanide Derivative of met80Ala-Iso-1-Cytochrome C
  Bren, K.L., Gray, H.B., Banci, L., Bertini, I., Turano, P.
  () To be published --: --

• Structurally Engineered Cytochromes with Unusual Ligand-Binding Properties: Expression of Saccharomyces Cerevisiae met80-->Ala Iso-1-Cytochrome C
  Lu, Y., Casimilo, D.R., Bren, K.L., Richards, J.H., Gray, H.B.
  (1993) Proc Natl Acad Sci U S A 90: 11456

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Organizational Affiliation: 

Department of Chemistry, University of Florence, Italy.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FERRICYTOCHROME C	A	108	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P00044 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P00044  Go to UniProtKB:  P00044

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
CYN	B [auth A]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	A	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 17 
• OLDERADO: 1FHB Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-06-16 
• Released Date: 1995-09-15 
Deposition Author(s): Banci, L., Bertini, I., Bren, K.L., Gray, H.B., Sompornpisut, P., Turano, P.

Revision History  

• Version 1.0: 1995-09-15
  Type: Initial release
  
• Version 1.1: 2008-03-21
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Data collection, Database references, Derived calculations, Other