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 
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 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Chitinase-3-like protein 1 | 361 | Ovis aries | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for Q6TMG6 (Ovis aries) Explore Q6TMG6  Go to UniProtKB:  Q6TMG6 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q6TMG6 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by: Sequence | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Tripeptide | B [auth P] | 3 | N/A | Mutation(s): 0  | |
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 Name | Purpose |
---|---|
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
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 (Full details and data files)
- 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