2G8Z | pdb_00002g8z

Crystal structure of the ternary complex of signalling protein from sheep (SPS-40) with trimer and designed peptide at 2.5A resolution

PDB DOI: https://doi.org/10.2210/pdb2G8Z/pdb

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

Deposited: 2006-03-04 Released: 2006-04-04
Deposition Author(s): Ethayathulla, A.S., Srivastava, D.B., Kumar, J., Somvanshi, R.K., Sharma, S., Singh, T.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.211 (Depositor)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.2 of the entry. See complete history.

Literature

Crystal structure of the ternary complex of signalling protein from sheep (SPS-40) with trimer and designed peptide at 2.5A resolution

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

To be published.

Macromolecule Content

Total Structure Weight: 42.64 kDa
Atom Count: 3,151
Modeled Residue Count: 364
Deposited Residue Count: 364
Unique protein chains: 2

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6TMG6
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth B]	5		N-Glycosylation	Interactions Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G21381MC GlyCosmos: G21381MC GlyGen: G21381MC

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	D [auth C]	3		N/A	Interactions Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G47362BJ GlyCosmos: G47362BJ GlyGen: G47362BJ

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900017 Query on PRD_900017	D [auth C]	triacetyl-beta-chitotriose	Oligosaccharide / Inhibitor		Interactions Focus chain D [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.211 (Depositor)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.87	α = 90
b = 66.26	β = 90
c = 107.498	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-04-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-04-04
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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-10-30
Changes: Structure summary