3QND

crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A potent trivalent sialic Acid inhibitor of adenovirus type 37 infection of human corneal cells.

Spjut, S.Qian, W.Bauer, J.Storm, R.Frangsmyr, L.Stehle, T.Arnberg, N.Elofsson, M.

(2011) Angew Chem Int Ed Engl 50: 6519-6521


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fiber protein194Human adenovirus D37Mutation(s): 0 
Gene Names: L5
UniProt
Find proteins for Q64823 (Human adenovirus D37)
Explore Q64823 
Go to UniProtKB:  Q64823
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64823
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SIA
Query on SIA

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
O [auth E]
Q [auth F]
H [auth A],
J [auth B],
L [auth C],
O [auth E],
Q [auth F],
S [auth G]
N-acetyl-alpha-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A]
I [auth B]
K [auth C]
M [auth E]
N [auth E]
G [auth A],
I [auth B],
K [auth C],
M [auth E],
N [auth E],
P [auth F],
R [auth G]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
SIA PDBBind:  3QND Kd: 1.40e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.19α = 90
b = 108.645β = 90
c = 112.511γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-10
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary