2XA5

Structure of substrate binding protein SiaP (A11N) in complex with Neu5Ac


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

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: 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 ...

    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

    Department of Chemical Biology & Therapeutics, and Department of Structural Biology , St. Jude Children's Research Hospital , Memphis , Tennessee 38105 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SIALIC ACID-BINDING PERIPLASMIC PROTEIN SIAPA312Haemophilus influenzaeMutation(s): 1 
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SLB
Query on SLB

Download Ideal Coordinates CCD File 
B [auth A]N-acetyl-beta-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-PFQGKNLYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.09 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.818α = 90
b = 74.7β = 90
c = 87.254γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-06
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Data collection, Version format compliance
  • Version 1.2: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-09-25
    Changes: Data collection, Database references, Other
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary