6ANN

Structure of cyclic D-Leu-N-methyl-D-Phe-2-Abz-D-Ala at 0.76 Angstrom

• PDB DOI: https://doi.org/10.2210/pdb6ANN/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2017-08-14 Released: 2017-11-15 
• Deposition Author(s): Cameron, A.J., Sarojini, V., Squire, C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.76 Å
• R-Value Free: 
  0.157 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Crystal and NMR Structures of a Peptidomimetic beta-Turn That Provides Facile Synthesis of 13-Membered Cyclic Tetrapeptides.

Cameron, A.J., Squire, C.J., Edwards, P.J.B., Harjes, E., Sarojini, V.

(2017) Chem Asian J 12: 3195-3202

• PubMed: 29098772 
• DOI: https://doi.org/10.1002/asia.201701422
• Primary Citation of Related Structures:  
  6ANM, 6ANN


• PubMed Abstract: 
  

  Herein we report the unique conformations adopted by linear and cyclic tetrapeptides (CTPs) containing 2-aminobenzoic acid (2-Abz) in solution and as single crystals. The crystal structure of the linear tetrapeptide H ₂ N-d-Leu-d-Phe-2-Abz-d-Ala-COOH (1) reveals a novel planar peptidomimetic β-turn stabilized by three hydrogen bonds and is in agreement with its NMR structure in solution. While CTPs are often synthetically inaccessible or cyclize in poor yield, both 1 and its N-Me-d-Phe analogue (2) adopt pseudo-cyclic frameworks enabling near quantitative conversion to the corresponding CTPs 3 and 4. The crystal structure of the N-methylated peptide (4) is the first reported for a CTP containing 2-Abz and reveals a distinctly planar 13-membered ring, which is also evident in solution. The N-methylation of d-Phe results in a peptide bond inversion compared to the conformation of 3 in solution.

---

Organizational Affiliation: 

School of Chemical Sciences, The University of Auckland, Auckland, 1142, New Zealand.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.55 kDa 
• Atom Count: 230 
• Modelled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cyclic DLE-ZAE-BE2-DAL	A, B, C, D, E	4	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EOH	F [auth A], G [auth B], H [auth D]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.76 Å
• R-Value Free:  0.157 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 14.502	α = 90
b = 21.962	β = 90
c = 45.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-15 
Deposition Author(s): Cameron, A.J., Sarojini, V., Squire, C.J.

Revision History  

• Version 1.0: 2017-11-15
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references
• Version 1.2: 2018-01-03
  Changes: Database references
• Version 2.0: 2021-09-15
  Changes: Atomic model, Database references, Derived calculations
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations