5I4F

scFv 2D10 complexed with alpha 1,6 mannobiose

• PDB DOI: https://doi.org/10.2210/pdb5I4F/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-12 Released: 2016-12-21 
• Deposition Author(s): Vashisht, S., Kumar, A., Kaur, K.J., Salunke, D.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.193 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 

Starting Model: experimental

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5VF2

Literature

Antibodies Can Exploit Molecular Crowding to Bind New Antigens at Noncanonical Paratope Positions

Vashisht, S., Kumar, A., Kaur, K.J., Salunke, D.M.

(2016) ChemistrySelect 1: 6287-6292

• DOI: https://doi.org/10.1002/slct.201600945

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.58 kDa 
• Atom Count: 2,189 
• Modelled Residue Count: 237 
• Deposited Residue Count: 251 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv 2D10	A	251	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose	B, C	2		N/A
Glycosylation Resources
GlyTouCan:  G77384RA GlyCosmos:  G77384RA GlyGen:  G77384RA

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900118	B, C	6alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.193 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.093	α = 90
b = 81.093	β = 90
c = 74.388	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Vashisht, S., Kumar, A., Kaur, K.J., Salunke, D.M.

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary