1LCM | pdb_00001lcm

NMR minimized average structure of microcystin-LR

• PDB DOI: https://doi.org/10.2210/pdb1LCM/pdb

• Classification: TOXIN, HYDROLASE INHIBITOR
• Organism(s): Microcystis aeruginosa
• Mutation(s): No 


• Deposited: 1995-12-30 Released: 1996-12-07 
• Deposition Author(s): Trogen, G., Zdunek, J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: MINIMIZED AVERAGE 

Literature

Conformational studies of microcystin-LR using NMR spectroscopy and molecular dynamics calculations.

Trogen, G.B., Annila, A., Eriksson, J., Kontteli, M., Meriluoto, J., Sethson, I., Zdunek, J., Edlund, U.

(1996) Biochemistry 35: 3197-3205

• PubMed: 8605154 
• DOI: https://doi.org/10.1021/bi952368s
• Primary Citation Related Structures: 
  1LCM


• PubMed Abstract: 
  

  NMR spectroscopy in aqueous and dimethyl sulfoxide/water solutions is used to determine the three-dimensional structures of microcystin-LR, a cyclic cyanobacterial heptapeptide toxin which is a potent inhibitor of type 1 and type 2A protein phosphatases. The conformations of this toxic peptide are studied using a simulated annealing (SA) protocol followed by refined SA calculations in vacuo and free MD simulations in water. Only one conformational family in each solvent is found. The peptide ring has a saddle-shaped form, essentially the same in both solvents. The structural difference observed between the two solution structures is located to the part consisting of Mdha, Ala, and Leu. This peptide segment is not present in nodularin, a cyclic pentapeptide of similar toxicity. The Arg side chain is very flexible, while the side chain of Leu is well defined. The side chain of Adda, essential for toxicity, is constrained in the vicinity of the backbone ring but appears to be flexible in the more remote part.

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Organizational Affiliation: 
• Department of Organic Chemistry, Umea University, Sweden.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 1.01 kDa 
• Atom Count: 70 
• Modeled Residue Count: 7 
• Deposited Residue Count: 7 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
microcystin LR	A	7	Microcystis aeruginosa	Mutation(s): 0

Small Molecules

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
1ZN	A	PEPTIDE-LIKE	C20 H29 N O3		--
DAL	A	D-PEPTIDE LINKING	C3 H7 N O2		--
DAM	A	PEPTIDE LINKING	C4 H7 N O2		--

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000212	A	Microcystin LR	Oligopeptide / Toxin

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 1 
• Selection Criteria: MINIMIZED AVERAGE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-12-07 
Deposition Author(s): Trogen, G., Zdunek, J.

Revision History  

• Version 1.0: 1996-12-07
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Database references, Derived calculations, Non-polymer description, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2013-02-06
  Changes: Derived calculations
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other