2QF8

Crystal structure of the complex of Buffalo Secretory Glycoprotein with tetrasaccharide at 2.8A resolution

• PDB DOI: https://doi.org/10.2210/pdb2QF8/pdb

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


• Deposited: 2007-06-27 Released: 2007-07-10 
• Deposition Author(s): Singh, A.K., Jain, R., Sinha, M., Kumar, A., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.227 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Starting Model: experimental

Literature

Crystal structure of the complex of Buffalo Secretory Glycoprotein with Tetrasaccharide at 2.8A resolution

Singh, A.K., Jain, R., Sinha, M., Kumar, A., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.99 kDa 
• Atom Count: 3,109 
• 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	B	4		N/A
Glycosylation Resources
GlyTouCan:  G01361SX GlyCosmos:  G01361SX GlyGen:  G01361SX

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: 0.227 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• 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
REFMAC	refinement
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-10 
Deposition Author(s): Singh, A.K., Jain, R., Sinha, M., Kumar, A., Singh, N., Sharma, S., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2007-07-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-04-15
  Changes: Data collection, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-20
  Changes: Structure summary