1KMG

The Solution Structure Of Monomeric Copper-free Superoxide Dismutase

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 35 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure and dynamics of copper-free SOD: The protein before binding copper.

Banci, L., Bertini, I., Cantini, F., D'Onofrio, M., Viezzoli, M.S.

(2002) Protein Sci 11: 2479-2492

  • DOI: 10.1110/ps.0210802
  • Primary Citation of Related Structures:  
    1KMG

  • PubMed Abstract: 

    • The solution structure of the copper-free state of a monomeric form of superoxide dismutase (153 amino acids) was determined through (13)C and (15)N labeling. The protein contained two mutations at the native subunit-subunit interface (F50E and G51E) to obtain a soluble monomeric species and a mutation in the active site channel (E133Q) ...

    The solution structure of the copper-free state of a monomeric form of superoxide dismutase (153 amino acids) was determined through (13)C and (15)N labeling. The protein contained two mutations at the native subunit-subunit interface (F50E and G51E) to obtain a soluble monomeric species and a mutation in the active site channel (E133Q). About 93% of carbon atoms, 95% of nitrogen atoms, and 96% of the protons were assigned. A total of 2467 meaningful NOEs and 170 dihedral angles provided a family of 35 conformers with RMSD values of 0.76 +/- 0.09 A for the backbone and 1.22 +/- 0.13 A for all heavy atoms. The secondary structure elements, connected by loops, produce the typical superoxide dismutase Greek key fold, formed by an eight-stranded beta-barrel. The comparison with the copper-bound monomeric and dimeric structures shows that the metal ligands have a conformation very close to that of the copper-bound forms. This feature indicates that the copper-binding site is preorganized and well ordered also in the absence of the copper ion. The active-site channel shows a sizable increase in width, achieving a suitable conformation to receive the copper ion. The histidines ring NH resonances that bind the copper ion and the region around the active-site channel experience, as found from (15)N relaxation studies, conformational exchange processes. The increased width of the channel and the higher mobility of the histidine rings of the copper site in the copper-free form with respect to the holoprotein is discussed in terms of the process of copper insertion.

    Organizational Affiliation: 

    The Magnetic Resonance Center (CERM) and Department of Chemistry, University of Florence, 50019, Sesto Fiorentino, Italy.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Superoxide DismutaseA153Homo sapiensMutation(s): 5 
Gene Names: SOD1
EC: 1.15.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00441 (Homo sapiens)
Explore P00441 
Go to UniProtKB:  P00441
PHAROS:  P00441
GTEx:  ENSG00000142168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00441
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 35 
  • Selection Criteria: target function 
  • OLDERADO: 1KMG Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Data collection, Database references, Derived calculations