5YYB

Crystal structure of Sialic acid Binding protein from Haemophilus ducreyi with Neu5Gc

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative ABC transporter periplasmic binding protein
A, B
482[Haemophilus] ducreyi 35000HPMutation(s): 0 
Gene Names: HD_1669
UniProt
Find proteins for Q7VL18 (Haemophilus ducreyi (strain 35000HP / ATCC 700724))
Explore Q7VL18 
Go to UniProtKB:  Q7VL18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7VL18
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NGE
Query on NGE
Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]		N-glycolyl-beta-neuraminic acid
C11 H19 N O10
FDJKUWYYUZCUJX-AJKRCSPLSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
NGE Binding MOAD:  5YYB Kd: 277 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.176 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.413α = 90
b = 70.125β = 114.24
c = 113.081γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
Aimlessdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
IndiaSR/SO/BB-19/2010
IndiaBT/IN/Sweden/41/SR/2013

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary