1R9V | pdb_00001r9v

NMR Structure of a D,L-Alternating Dodecamer of Norleucine

• PDB DOI: https://doi.org/10.2210/pdb1R9V/pdb
• BMRB: 6039

• Classification: DE NOVO PROTEIN
• Mutation(s): No 


• Deposited: 2003-10-31 Released: 2003-12-02 
• Deposition Author(s): Navarro, E., Celda, B.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 25 
• Conformers Submitted: 5 
• Selection Criteria: structures with the lowest energy 

Literature

Solution NMR Structure of a D,L-Alternating Oligonorleucine as a Model of Beta-Helix

Navarro, E., Tejero, R., Fenude, E., Celda, B.

(2001) Biopolymers 59: 110-119

• PubMed: 11373724 
• DOI: https://doi.org/10.1002/1097-0282(200108)59:2<110::AID-BIP1010>3.0.CO;2-S
• Primary Citation Related Structures: 
  1R9V


• PubMed Abstract: 
  

  beta-Helix structures are of particular interest due to their capacity to form transmembrane channels with different transport properties. However, the relatively large number of beta-helices configurations does not allow a direct conformational analysis of beta-helical oligopeptides. A synthetic alternating D,L-oligopeptide with twelve norleucines (XIIMe) has been used as a model to get insight in the conformational features of beta-helix structures. The spatial configuration of XIIMe in solution has been determined by NMR. An extensive set of distances (nuclear Overhauser effect) and dihedral (J coupling constants) constraints have been included in molecular dynamics calculations. The NMR experimental data and theoretical calculations clearly indicate that the XIIMe adopts a single beta(4.4)-helix-type conformation in nonpolar solvents.

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Organizational Affiliation: 
• Departamento de Química Física, Facultat de Químicas, Universitat de Valencia, C/Dr. Moliner, 50, 46100-Burjassot (Valencia), Spain.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 1.5 kDa 
• Atom Count: 98 
• Modeled Residue Count: 12 
• Deposited Residue Count: 13 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BOC-(D-NLE-L-NLE)4-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTER	A	13	N/A	Mutation(s): 0

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DNE	A	D-PEPTIDE LINKING	C6 H13 N O2		--
DNM	A	D-PEPTIDE LINKING	C7 H15 N O2		--
NLE	A	L-PEPTIDE LINKING	C6 H13 N O2		LEU
NLO	A	L-PEPTIDE LINKING	C7 H15 N O2		LEU

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000106	A	BOC-(D-NLE-L-NLE)4-D-NLE(METHYL)-L-NLE-D-NLE-L-NLE METHYL ESTER	Polypeptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 25 
• Conformers Submitted: 5 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-12-02 
Deposition Author(s): Navarro, E., Celda, B.

Revision History  

• Version 1.0: 2003-12-02
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2022-02-09
  Changes: Data collection, Database references, Derived calculations
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations