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 8IDM

Crystal structure of nanobody VHH-227 with nanobody VHH-T71 and MERS-CoV RBD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 

Starting Models: experimental
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This is version 1.1 of the entry. See complete history. 


Literature

Structural Definition of a Novel Nanobody Binding Site specifically targeting the MERS-CoV RBD Core-Domain with Neutralizing Capacity

Idoudi, F., Wang, R., Tian, L., Zhang, L., Wang, X.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VHH-227A [auth B]135Camelus dromedariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence AnnotationsExpand
  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VHH-T71B [auth A]136Camelus dromedariusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence AnnotationsExpand
  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1C [auth D]229Middle East respiratory syndrome-related coronavirusMutation(s): 0 
UniProt
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N5Q8 
Go to UniProtKB:  K9N5Q8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9N5Q8
Glycosylation
Glycosylation Sites: 2
Sequence AnnotationsExpand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranoseD [auth C]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG
Download Ideal Coordinates CCD File 
F [auth D]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.254 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.44α = 90
b = 104.44β = 90
c = 318.223γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Structure summary