5X52

Human serum albumin complexed with octanoate and N-acetyl-L-methionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystallographic analysis of the ternary complex of octanoate and N-acetyl-l-methionine with human serum albumin reveals the mode of their stabilizing interactions

Kawai, A.Chuang, V.T.G.Kouno, Y.Yamasaki, K.Miyamoto, S.Anraku, M.Otagiri, M.

(2017) Biochim. Biophys. Acta 1865: 979-984

  • DOI: 10.1016/j.bbapap.2017.04.004

  • PubMed Abstract: 
  • During pasteurization and storage of albumin products, Sodium octanoate (Oct) and N-acethyl-l-tryptophan (N-AcTrp) are used as the thermal stabilizer and the antioxidant for human serum albumin (HSA), respectively. We recently reported that N-acethyl ...

    During pasteurization and storage of albumin products, Sodium octanoate (Oct) and N-acethyl-l-tryptophan (N-AcTrp) are used as the thermal stabilizer and the antioxidant for human serum albumin (HSA), respectively. We recently reported that N-acethyl-l-methionine (N-AcMet) is an antioxidant for HSA, which is superior to N-AcTrp when it is especially exposed to light during storage. The objective of the present study is to clarify the molecular mechanism responsible for the HSA protective effect of Oct and N-AcMet based on their ternary complex structure. Crystal structure of the HSA-Oct-N-AcMet complex showed that one N-AcMet molecule is bound to the entrance of drug site 1 of HSA, and its side chain, which is susceptible to the oxidation, is exposed to the solvent. At the same time, two Oct binding sites are observed in drug sites 1 and 2 of HSA, respectively, and each Oct molecule occupies the hydrophobic cavity in them. These results indicate the molecular mechanism responsible for the HSA stabilization by these small molecules as follows. N-AcMet seals the entrance of drug site 1 while it acts as an antioxidant for HSA. Oct is chiefly bound to drug site 2 of HSA and it increases the thermal stability of HSA because of the occupying the largest intra-cavity of sub-domain IIIA in HSA. These findings suggest that N-AcMet acts positively as useful stabilizer for albumin formulated products such as functionalized HSA and HSA fusion proteins.


    Organizational Affiliation

    Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan; DDS Research Institute, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan. Electronic address: otagirim@ph.sojo-u.ac.jp.,Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan.,Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan; DDS Research Institute, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan.,School of Pharmacy, Faculty of Health Sciences, Curtin University, GPO Box U1987, Perth 6845, WA, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serum albumin
A, B
585Homo sapiensMutation(s): 0 
Gene Names: ALB
Find proteins for P02768 (Homo sapiens)
Go to Gene View: ALB
Go to UniProtKB:  P02768
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
AME
Query on AME

Download SDF File 
Download CCD File 
A, B
N-ACETYLMETHIONINE
C7 H13 N O3 S
XUYPXLNMDZIRQH-LURJTMIESA-N
 Ligand Interaction
OCA
Query on OCA

Download SDF File 
Download CCD File 
A, B
OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.005 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.236 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.538α = 90.00
b = 179.373β = 105.43
c = 59.323γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-02-14 
  • Released Date: 2017-05-17 
  • Deposition Author(s): Kawai, A., Otagiri, M.

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Database references