6V8S | pdb_00006v8s

Crystal structure of Ara h 8.0201


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.266 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 
    0.234 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of 8-anilino-1-naphthalene sulfonate (ANS) binding to the PR-10 allergen Ara h 8.

O'Malley, A.Offermann, L.R.Khatri, K.Linn, C.Pote, S.McBride, J.K.Perdue, M.L.Hurlburt, B.K.Maleki, S.J.Mias, G.I.Chruszcz, M.

(2025) Biochem Biophys Res Commun 793: 153013-153013

  • DOI: https://doi.org/10.1016/j.bbrc.2025.153013
  • Primary Citation Related Structures: 
    6AWR, 6V8H, 6V8J, 6V8M, 6V8S

  • PubMed Abstract: 

    We previously determined crystal structures of peanut allergen Ara h 8.0101 in the apo form as well as in complex with model ligands. These structures illustrated the varied ligand binding capabilities of PR-10s and Ara h 8's structural similarity to the major birch allergen Bet v 1. Here, we expanded on those structural studies with structures of Ara h 8.0101 and Ara h 8.0201 in complex with 8-anilino-1-naphthalene sulfonate (ANS), as well as the apo form of Ara h 8.0201. Structural studies revealed that both proteins may bind more than one ANS molecule. We also examined the impact of ANS on the ligand binding cavities of Ara h 8.0101 and Ara h 8.0201 with fluorescence assays and compared the results to prototypic PR-10 Bet v 1.0101. Moreover, as ANS is often used in fluorescence-based ligand binding assays, we analyzed structures from the PDB and provided a summary on experimentally determined ANS binding sites. These analyses show that ANS is useful for investigation of ligand binding sites, but it may also participate in non-specific reactions on nonpolar surfaces of proteins.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.

Macromolecule Content 

  • Total Structure Weight: 293.55 kDa 
  • Atom Count: 21,480 
  • Modeled Residue Count: 2,430 
  • Deposited Residue Count: 2,448 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ara h 8 allergen isoform
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
153Arachis hypogaeaMutation(s): 0 
Gene Names: Ahy_Scaffold6g108211
UniProt
Find proteins for B0YIU5 (Arachis hypogaea)
Explore B0YIU5 
Go to UniProtKB:  B0YIU5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0YIU5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2AN
(Subject of Investigation/LOI)

Query on 2AN



Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth F]
AC [auth J]
AD [auth N]
BA [auth C]
AA [auth C],
AB [auth F],
AC [auth J],
AD [auth N],
BA [auth C],
BB [auth F],
BC [auth J],
BD [auth N],
CA [auth C],
CB [auth F],
CC [auth J],
CD [auth O],
DA [auth C],
DB [auth G],
DC [auth J],
DD [auth O],
EA [auth C],
EB [auth G],
EC [auth K],
ED [auth O],
FA [auth C],
FB [auth G],
FC [auth K],
FD [auth O],
GA [auth C],
GB [auth G],
GC [auth K],
GD [auth P],
HA [auth C],
HB [auth G],
HC [auth K],
HD [auth P],
IA [auth D],
IB [auth G],
IC [auth K],
ID [auth P],
JA [auth D],
JB [auth H],
JC [auth K],
JD [auth P],
KA [auth D],
KB [auth H],
KC [auth K],
KD [auth P],
LA [auth D],
LB [auth H],
LC [auth L],
LD [auth P],
MA [auth D],
MB [auth H],
MC [auth L],
MD [auth P],
NA [auth D],
NB [auth H],
NC [auth L],
ND [auth P],
OA [auth E],
OB [auth H],
OC [auth L],
OD [auth P],
PA [auth E],
PB [auth H],
PC [auth M],
Q [auth A],
QA [auth E],
QB [auth H],
QC [auth M],
R [auth A],
RA [auth E],
RB [auth H],
RC [auth M],
S [auth A],
SA [auth E],
SC [auth M],
T [auth A],
TA [auth E],
TB [auth I],
TC [auth M],
U [auth A],
UA [auth E],
UB [auth I],
UC [auth M],
V [auth B],
VA [auth F],
VB [auth I],
VC [auth M],
W [auth B],
WA [auth F],
WB [auth I],
WC [auth M],
X [auth B],
XA [auth F],
XB [auth I],
XC [auth M],
Y [auth B],
YA [auth F],
YB [auth J],
YC [auth N],
Z [auth C],
ZA [auth F],
ZB [auth J],
ZC [auth N]
8-ANILINO-1-NAPHTHALENE SULFONATE
C16 H13 N O3 S
FWEOQOXTVHGIFQ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
SB [auth H]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.266 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.239 (DCC) 
  • R-Value Observed: 0.234 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.161α = 94.13
b = 90.027β = 106.91
c = 94.245γ = 97.23
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2025-12-03
    Changes: Database references, Structure summary