4ML4

Crystal structure of the complex of signaling glycoprotein from buffalo (SPB-40) with tetrahydropyran at 2.5 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4ML4/pdb

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


• Deposited: 2013-09-06 Released: 2013-09-25 
• Deposition Author(s): Yamini, S., Chaudhary, A., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 

Starting Model: experimental

Literature

Crystal structure of the complex of signaling glycoprotein from buffalo (SPB-40) with tetrahydropyran at 2.5 A resolution

Yamini, S., Chaudhary, A., 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: 41.25 kDa 
• Atom Count: 3,038 
• 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PYE	C [auth A]	TETRAHYDROPYRAN C5 H10 O DHXVGJBLRPWPCS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.263 
• R-Value Work: 0.247 
• R-Value Observed: 0.247 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.174	α = 90
b = 67.088	β = 90
c = 106.569	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Yamini, S., Chaudhary, A., Sinha, M., Kaur, P., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.3: 2024-11-06
  Changes: Structure summary