3V09 | pdb_00003v09

Crystal structure of Rabbit Serum Albumin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.243 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.3 of the entry. See complete history

Literature

Structural and immunologic characterization of bovine, horse, and rabbit serum albumins.

Majorek, K.A.Porebski, P.J.Dayal, A.Zimmerman, M.D.Jablonska, K.Stewart, A.J.Chruszcz, M.Minor, W.

(2012) Mol Immunol 52: 174-182

  • DOI: https://doi.org/10.1016/j.molimm.2012.05.011
  • Primary Citation Related Structures: 
    3V03, 3V08, 3V09

  • PubMed Abstract: 

    Serum albumin (SA) is the most abundant plasma protein in mammals. SA is a multifunctional protein with extraordinary ligand binding capacity, making it a transporter molecule for a diverse range of metabolites, drugs, nutrients, metals and other molecules. Due to its ligand binding properties, albumins have wide clinical, pharmaceutical, and biochemical applications. Albumins are also allergenic, and exhibit a high degree of cross-reactivity due to significant sequence and structure similarity of SAs from different organisms. Here we present crystal structures of albumins from cattle (BSA), horse (ESA) and rabbit (RSA) sera. The structural data are correlated with the results of immunological studies of SAs. We also analyze the conservation or divergence of structures and sequences of SAs in the context of their potential allergenicity and cross-reactivity. In addition, we identified a previously uncharacterized ligand binding site in the structure of RSA, and calcium binding sites in the structure of BSA, which is the first serum albumin structure to contain metal ions.


  • Organizational Affiliation
    • Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.

Macromolecule Content 

  • Total Structure Weight: 69.71 kDa 
  • Atom Count: 4,822 
  • Modeled Residue Count: 583 
  • Deposited Residue Count: 584 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serum albumin584Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P49065 (Oryctolagus cuniculus)
Explore P49065 
Go to UniProtKB:  P49065
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49065
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES

Query on MES



Download:Ideal Coordinates CCD File
B [auth A],
E [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
HA [auth A]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
GA [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
UNX

Query on UNX



Download:Ideal Coordinates CCD File
AA [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
AA [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
UNKNOWN ATOM OR ION
X

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.463α = 90
b = 81.884β = 90
c = 104.851γ = 90
Software Package:
Software NamePurpose
BLU-MAXdata collection
HKL-3000phasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-10-10
    Changes: Database references
  • Version 2.0: 2018-01-10
    Changes: Advisory, Atomic model, Non-polymer description, Structure summary
  • Version 2.1: 2022-04-13
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2023-09-13
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-10-30
    Changes: Structure summary