5H47 | pdb_00005h47

Crystal structure of AOL complexed with 2-MeSe-Fuc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.258 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5H47

Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Synthesis of seleno-fucose compounds and their application to the X-ray structural determination of carbohydrate-lectin complexes using single/multi-wavelength anomalous dispersion phasing

Shimabukuro, J.Makyio, H.Suzuki, T.Nishikawa, Y.Kawasaki, M.Imamura, A.Ishida, H.Ando, H.Kato, R.Kiso, M.

(2017) Bioorg Med Chem 25: 1132-1142

  • DOI: https://doi.org/10.1016/j.bmc.2016.12.021
  • Primary Citation Related Structures: 
    5H47

  • PubMed Abstract: 

    Selenium-incorporated fucoses (seleno-fucoses) differing in the position of the seleno-substituent were synthesized and applied to the X-ray structural determination of a carbohydrate-lectin complex using single/multi-wavelength anomalous dispersion (SAD/MAD) phasing. The hydroxyl groups at the C-1, -2, -3 and -4 position of fucose were individually substituted with a methylseleno group via a transacetalization reaction using MeSeCH 2 OBn or by an S N 2 reaction with TolSe - equivalents to afford the corresponding MeSe-fucose. The three-dimensional structures of a fucose-binding lectin complexed with several of these MeSe-fucoses have been determined by SAD/MAD phasing by utilizing the diffraction of selenium in the bound MeSe-fucoses.


  • Organizational Affiliation
    • Department of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan; Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan.

Macromolecule Content 

  • Total Structure Weight: 433.28 kDa 
  • Atom Count: 31,809 
  • Modeled Residue Count: 3,720 
  • Deposited Residue Count: 3,732 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
311Aspergillus oryzae RIB40Mutation(s): 0 
Gene Names: AO090001000189
UniProt
Find proteins for Q2UNX8 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore Q2UNX8 
Go to UniProtKB:  Q2UNX8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2UNX8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FSW

Query on FSW



Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth G]
AC [auth L]
BA [auth C]
BB [auth G]
AA [auth C],
AB [auth G],
AC [auth L],
BA [auth C],
BB [auth G],
BC [auth L],
CA [auth C],
CB [auth H],
CC [auth L],
DA [auth C],
DB [auth H],
DC [auth L],
EA [auth D],
EB [auth H],
EC [auth L],
FA [auth D],
FB [auth H],
FC [auth L],
GA [auth D],
GB [auth H],
HA [auth D],
HB [auth H],
IA [auth D],
IB [auth I],
JA [auth D],
JB [auth I],
KA [auth E],
KB [auth I],
LA [auth E],
LB [auth I],
M [auth A],
MA [auth E],
MB [auth I],
N [auth A],
NA [auth E],
NB [auth I],
O [auth A],
OA [auth E],
OB [auth J],
P [auth A],
PA [auth E],
PB [auth J],
Q [auth A],
QA [auth F],
QB [auth J],
R [auth A],
RA [auth F],
RB [auth J],
S [auth B],
SA [auth F],
SB [auth J],
T [auth B],
TA [auth F],
TB [auth J],
U [auth B],
UA [auth F],
UB [auth K],
V [auth B],
VA [auth F],
VB [auth K],
W [auth B],
WA [auth G],
WB [auth K],
X [auth B],
XA [auth G],
XB [auth K],
Y [auth C],
YA [auth G],
YB [auth K],
Z [auth C],
ZA [auth G],
ZB [auth K]
methyl 6-deoxy-2-Se-methyl-2-seleno-alpha-L-galactopyranoside
C8 H16 O4 Se
GFGVRXDXSFUDNW-FMGWEMOISA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.258 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.972α = 90
b = 214.316β = 108.24
c = 126.531γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-15
    Changes: Database references
  • Version 1.2: 2017-08-30
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 1.4: 2024-03-20
    Changes: Data collection, Database references, Structure summary