4MTV

Crystal structure of the complex of Buffalo Signalling Glycoprotein with pentasaccharide at 2.8A resolution

• PDB DOI: https://doi.org/10.2210/pdb4MTV/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Bubalus bubalis
• Mutation(s): No 


• Deposited: 2013-09-20 Released: 2013-10-16 
• Deposition Author(s): Shukla, P.K., Chaudhary, A., Singh, A.K., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Crystal structure of the complex of Buffalo Signalling Glycoprotein with pentasaccharide at 2.8A resolution

Shukla, P.K., Chaudhary, A., Singh, A.K., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.2 kDa 
• Atom Count: 3,073 
• Modelled Residue Count: 361 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chitinase-3-like protein 1	A	361	Bubalus bubalis	Mutation(s): 0
UniProt
Find proteins for Q7YS85 (Bubalus bubalis) Explore Q7YS85  Go to UniProtKB:  Q7YS85
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan:  G07670VS GlyCosmos:  G07670VS GlyGen:  G07670VS

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.87	α = 90
b = 66.499	β = 90
c = 107.126	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
AUTOMAR	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Shukla, P.K., Chaudhary, A., Singh, A.K., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary