6NOM | pdb_00006nom

NMR solution structure of Pisum sativum defensin 2 (Psd2) provides evidence for the presence of hydrophobic surface clusters

• PDB DOI: https://doi.org/10.2210/pdb6NOM/pdb
• BMRB: 30561

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Lathyrus oleraceus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2019-01-16 Released: 2019-08-21 
• Deposition Author(s): Pinheiro-Aguiar, R., Amaral, V.S.G., Bastos, I., Kurtenbach, E., Almeida, F.C.L.
• Funding Organization(s): Brazilian National Council for Scientific and Technological Development (CNPq)

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Nuclear magnetic resonance solution structure of Pisum sativum defensin 2 provides evidence for the presence of hydrophobic surface-clusters.

Pinheiro-Aguiar, R., do Amaral, V.S.G., Pereira, I.B., Kurtenbach, E., Almeida, F.C.L.

(2020) Proteins 88: 242-246

• PubMed: 31294889 
• DOI: https://doi.org/10.1002/prot.25783
• Primary Citation Related Structures: 
  6NOM


• PubMed Abstract: 
  

  Pisum sativum defensin 2 (Psd2) is a small (4.7 kDa) antifungal peptide whose structure is held together by four conserved disulfide bridges. Psd2 shares the cysteine-stabilized alpha-beta (CSαβ) fold, which lacks a regular hydrophobic core. All hydrophobic residues are exposed to the surface, except for leucine 6. They are clustered in the surface formed by two loops, between β1 and α-helix and β2 and β3 sheets. The observation of surface hydrophobic clusters reveals a remarkable evolution of the CSαβ fold to expose and reorganize hydrophobic residues, which facilitates creating versatile binding sites.

---

Organizational Affiliation: 
• Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil.
Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil.
Campus Macaé Professor Aloísio Teixeira, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brasil.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 5.41 kDa 
• Atom Count: 372 
• Modeled Residue Count: 47 
• Deposited Residue Count: 47 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Defensin-2	A	47	Lathyrus oleraceus	Mutation(s): 0
UniProt
Find proteins for P81930 (Pisum sativum) Explore P81930  Go to UniProtKB:  P81930

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Pinheiro-Aguiar, R., Amaral, V.S.G., Bastos, I., Kurtenbach, E., Almeida, F.C.L.

---

Funding Organization	Location	Grant Number
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	209306/2013-2
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	457773/2014-6

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Database references
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-06-14
  Changes: Database references, Derived calculations, Other
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Structure summary