2ARX
Pterocarpus angolensis seed lectin in complex with the decasaccharide NA2F
- PDB DOI: https://doi.org/10.2210/pdb2ARX/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Pterocarpus angolensis
- Mutation(s): No
- Deposited: 2005-08-22 Released: 2006-08-01
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.216
- R-Value Work: 0.176
- R-Value Observed: 0.179
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 |
| lectin | 252 | Pterocarpus angolensis | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for Q8GSD2 (Pterocarpus angolensis) Explore Q8GSD2 Go to UniProtKB: Q8GSD2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8GSD2 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose | C | 2 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G00891MP GlyCosmos: G00891MP GlyGen: G00891MP | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose | D | 7 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G18830JZ GlyCosmos: G18830JZ GlyGen: G18830JZ | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | G [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| MN Query on MN | E [auth A], H [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| CA Query on CA | F [auth A], I [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900112 Query on PRD_900112 | C | 3alpha-alpha-mannobiose | Oligosaccharide / Metabolism |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.216
- R-Value Work: 0.176
- R-Value Observed: 0.179
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.78 | α = 90 |
| b = 83.32 | β = 90 |
| c = 122.38 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
| CNS | refinement |
Entry History
Deposition Data
- Released Date: 2006-08-01 Deposition Author(s): Buts, L., Garcia-Pino, A., Imberty, A., Amiot, N., Boons, G.-J., Lah, J., Versees, W., Wyns, L., Loris, R.
Revision History (Full details and data files)
- Version 1.0: 2006-08-01
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2012-02-22
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary
