1L4V | pdb_00001l4v

SOLUTION STRUCTURE OF SAPECIN

• PDB DOI: https://doi.org/10.2210/pdb1L4V/pdb
• BMRB: 1209

• Classification: ANTIBIOTIC
• Organism(s): Sarcophaga peregrina
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2002-03-06 Released: 2002-03-27 
• Deposition Author(s): Hanzawa, H., Iwai, H., Takeuchi, K., Kuzuhara, T., Komano, H., Kohda, D., Inagaki, F., Natori, S., Arata, Y., Shimada, I.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 18 
• Selection Criteria: structures with the lowest energy 

Literature

1H nuclear magnetic resonance study of the solution conformation of an antibacterial protein, sapecin.

Hanzawa, H., Shimada, I., Kuzuhara, T., Komano, H., Kohda, D., Inagaki, F., Natori, S., Arata, Y.

(1990) FEBS Lett 269: 413-420

• PubMed: 2401368 
• DOI: https://doi.org/10.1016/0014-5793(90)81206-4
• Primary Citation Related Structures: 
  1L4V


• PubMed Abstract: 
  

  The solution conformation of an antibacterial protein sapecin has been determined by 1H nuclear magnetic resonance (NMR) and dynamical simulated annealing calculations. It has been shown that the polypeptide fold consists of one flexible loop (residues 4-12), one helix (residues 15-23), and two extended strands (residues 24-31 and 34-40). It was found that the tertiary structure of sapecin is completely different from that of rabbit neutrophil defensin NP-5, which is homologous to sapecin in the amino acid sequences and also has the antibacterial activity. The three-dimensional structure determination has revealed that a basic-residue rich region and the hydrophobic surface face each other on the surface of sapecin.

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Organizational Affiliation: 
• Faculty of Pharmaceutical Sciences, University of Tokyo, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.09 kDa 
• Atom Count: 280 
• Modeled Residue Count: 40 
• Deposited Residue Count: 40 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sapecin	A	40	Sarcophaga peregrina	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P18313 (Sarcophaga peregrina) Explore P18313  Go to UniProtKB:  P18313

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 18 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-27 
Deposition Author(s): Hanzawa, H., Iwai, H., Takeuchi, K., Kuzuhara, T., Komano, H., Kohda, D., Inagaki, F., Natori, S., Arata, Y., Shimada, I.

Revision History  

• Version 1.0: 2002-03-27
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-02-23
  Changes: Database references, Derived calculations, Experimental preparation
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary