2PHF
Pterocarpus angolensis lectin complexed with Man-6
- PDB DOI: https://doi.org/10.2210/pdb2PHF/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Pterocarpus angolensis
- Mutation(s): No
- Deposited: 2007-04-11 Released: 2007-07-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.216
- R-Value Work: 0.180
wwPDB Validation 3D Report Full Report
This is version 3.1 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
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MN Query on MN | E [auth A], G [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| CA Query on CA | F [auth A], H [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PCA Query on PCA | A, B | L-PEPTIDE LINKING | C5 H7 N O3 |  | GLN |
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: 2.10 Å
- R-Value Free: 0.216
- R-Value Work: 0.180
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.74 | α = 90 |
| b = 83.33 | β = 90 |
| c = 122.81 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345 | data collection |
| CNS | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2007-07-10 Deposition Author(s): Garcia-Pino, A., Buts, L., Wyns, L., Imberty, A., Loris, R.
Revision History (Full details and data files)
- Version 1.0: 2007-07-10
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 2.0: 2019-12-25
Changes: Database references, Derived calculations, Polymer sequence - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 3.1: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
