2E53
Crystal structure of basic winged bean lectin in complex with B blood group disaccharide
- PDB DOI: https://doi.org/10.2210/pdb2E53/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Psophocarpus tetragonolobus
- Mutation(s): No
- Deposited: 2006-12-18 Released: 2007-06-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.240
- R-Value Work: 0.202
- R-Value Observed: 0.202
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 |
| Basic agglutinin | 241 | Psophocarpus tetragonolobus | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for O24313 (Psophocarpus tetragonolobus) Explore O24313 Go to UniProtKB: O24313 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O24313 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | E, H, K, N, O | 4 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G18638YB GlyCosmos: G18638YB GlyGen: G18638YB | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | F | 3 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G11971MR GlyCosmos: G11971MR GlyGen: G11971MR | |||||
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-galactopyranose-(1-3)-alpha-D-galactopyranose | G, J, M, P | 2 |  | N/A | |
Glycosylation Resources | |||||
GlyTouCan: G91563HD GlyCosmos: G91563HD GlyGen: G91563HD | |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MN Query on MN | R [auth A], T [auth B], V [auth C], X [auth D] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| CA Query on CA | Q [auth A], S [auth B], U [auth C], W [auth D] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.240
- R-Value Work: 0.202
- R-Value Observed: 0.202
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 157.367 | α = 90 |
| b = 91.093 | β = 90 |
| c = 73.399 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNS | refinement |
| MAR345dtb | data collection |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 2007-06-26 Deposition Author(s): Kulkarni, K.A., Katiyar, S., Surolia, A., Vijayan, M., Suguna, K.
Revision History (Full details and data files)
- Version 1.0: 2007-06-26
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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary
