3QND

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

• PDB DOI: https://doi.org/10.2210/pdb3QND/pdb

• Classification: CELL ADHESION/INHIBITOR
• Organism(s): Human adenovirus D37
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-02-08 Released: 2011-06-15 
• Deposition Author(s): Stehle, T., Bauer, J., Elofsson, M.

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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

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

• PubMed: 21648036 
• DOI: https://doi.org/10.1002/anie.201101559
• Primary Citation of Related Structures:  
  3QND

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Organizational Affiliation: 

Department of Chemistry, Umeå Centre for Microbial Research (UCMR) and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90187 Umeå, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 132.61 kDa 
• Atom Count: 9,095 
• Modelled Residue Count: 1,104 
• Deposited Residue Count: 1,164 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fiber protein	A, B, C, D [auth E], E [auth F], F [auth G]	194	Human adenovirus D37	Mutation(s): 0  Gene Names: L5
UniProt
Find proteins for Q64823 (Human adenovirus D37) Explore Q64823  Go to UniProtKB:  Q64823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	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	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
ID	Source	Binding 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 = 105.19	α = 90
b = 108.645	β = 90
c = 112.511	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Stehle, T., Bauer, J., Elofsson, M.

Revision History  

• 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