Crystal structure of sialic acid binding protein

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.139 

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Water networks can determine the affinity of ligand binding to proteins.

Darby, J.F.Hopkins, A.P.Shimizu, S.Roberts, S.M.Brannigan, J.A.Turkenburg, J.P.Thomas, G.H.Hubbard, R.E.Fischer, M.

(2019) J Am Chem Soc 

  • DOI: https://doi.org/10.1021/jacs.9b06275
  • Primary Citation of Related Structures:  
    2V4C, 2WX9, 2WYK, 2WYP, 2XA5, 6H75, 6H76

  • PubMed Abstract: 

    Solvent organization is a key but underexploited contributor to the thermodynamics of protein-ligand recognition, with implications for ligand discovery, drug resistance, and protein engineering. Here, we explore the contribution of solvent to ligand binding in the Haemophilus influenzae virulence protein SiaP. By introducing a single mutation without direct ligand contacts, we observed a >1000-fold change in sialic acid binding affinity. Crystallographic and calorimetric data of wild-type and mutant SiaP showed that this change results from an enthalpically unfavorable perturbation of the solvent network. This disruption is reflected by changes in the normalized atomic displacement parameters of crystallographic water molecules. In SiaP's enclosed cavity, relative differences in water-network dynamics serve as a simple predictor of changes in the free energy of binding upon changing protein, ligand, or both. This suggests that solvent structure is an evolutionary constraint on protein sequence that contributes to ligand affinity and selectivity.

  • Organizational Affiliation

    Demuris Ltd., The Biosphere , Draymans Way, Newcastle Helix , Newcastle upon Tyne NE4 5BX , United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAP312Haemophilus influenzaeMutation(s): 1 
Find proteins for P44542 (Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd))
Explore P44542 
Go to UniProtKB:  P44542
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP44542
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on KDN

Download Ideal Coordinates CCD File 
B [auth A]deamino-beta-neuraminic acid
C9 H16 O9
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.139 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.836α = 90
b = 74.489β = 90
c = 88.151γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-09-25
    Changes: Data collection, Database references, Other, Structure summary
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary