2FDM

Crystal structure of the ternary complex of signalling glycoprotein frm sheep (SPS-40)with hexasaccharide (NAG6) and peptide Trp-Pro-Trp at 3.0A resolution

• PDB DOI: https://doi.org/10.2210/pdb2FDM/pdb

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


• Deposited: 2005-12-14 Released: 2006-01-10 
• Deposition Author(s): Srivastava, D.B., Ethayathulla, A.S., Kumar, J., Somvanshi, R.K., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

Crystal structure of the ternary complex of signalling glycoprotein frm sheep (SPS-40) with hexasaccharide (NAG6) and peptide Trp-Pro-Trp at 3.0A resolution

Srivastava, D.B., Ethayathulla, A.S., Kumar, J., Somvanshi, R.K., Sharma, S., Dey, S., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 42.76 kDa 
• Atom Count: 3,074 
• Modelled Residue Count: 364 
• Deposited Residue Count: 364 
• Unique protein chains: 2

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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tripeptide	B [auth P]	3	N/A	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG GlyCosmos:  G07375KG GlyGen:  G07375KG

Entity ID: 4
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-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	D [auth C]	6		N/A
Glycosylation Resources
GlyTouCan:  G17984VC GlyCosmos:  G17984VC GlyGen:  G17984VC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.230 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.497	α = 90
b = 66.624	β = 90
c = 107.481	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-10 
Deposition Author(s): Srivastava, D.B., Ethayathulla, A.S., Kumar, J., Somvanshi, R.K., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2006-01-10
  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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: 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: 2024-10-16
  Changes: Structure summary