5Z4V

Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40

• PDB DOI: https://doi.org/10.2210/pdb5Z4V/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Ovis aries
• Mutation(s): No 


• Deposited: 2018-01-15 Released: 2018-02-14 
• Deposition Author(s): Sharma, P., Singh, P.K., Singh, N., Sharma, S., Kaur, P., Betzel, C., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.188 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 

Starting Model: experimental

Literature

Crystal structure of the sheep signalling glycoprotein (SPS-40) complex with 2-methyl-2-4-pentanediol at 1.65A resolution reveals specific binding characteristics of SPS-40

Sharma, P., Singh, P.K., Singh, N., Sharma, S., Kaur, P., Betzel, C., 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: 41.21 kDa 
• Atom Count: 3,544 
• 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	Ovis aries	Mutation(s): 0
UniProt
Find proteins for Q6TMG6 (Ovis aries) Explore Q6TMG6  Go to UniProtKB:  Q6TMG6
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
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.188 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.873	α = 90
b = 66.415	β = 90
c = 105.692	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Sharma, P., Singh, P.K., Singh, N., Sharma, S., Kaur, P., Betzel, C., Singh, T.P.

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description, Structure summary