2FMD
Structural basis of carbohydrate recognition by Bowringia milbraedii seed agglutinin
- PDB DOI: https://doi.org/10.2210/pdb2FMD/pdb
- Classification: SUGAR BINDING PROTEIN
- Organism(s): Leucomphalos mildbraedii
- Mutation(s): No
- Deposited: 2006-01-09 Released: 2006-08-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.228
- R-Value Work: 0.183
- R-Value Observed: 0.186
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 |
| Lectin | 240 | Leucomphalos mildbraedii | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for P42088 (Leucomphalos mildbraedii) Explore P42088 Go to UniProtKB: P42088 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P42088 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Oligosaccharides
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MN Query on MN | D [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| CA Query on CA | C [auth A] | 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_900111 Query on PRD_900111 | B | 2alpha-alpha-mannobiose | Oligosaccharide / Metabolism |  | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.228
- R-Value Work: 0.183
- R-Value Observed: 0.186
- Space Group: I 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 66.603 | α = 90 |
| b = 86.351 | β = 90 |
| c = 91.76 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| CNS | refinement |
Entry History
Deposition Data
- Released Date: 2006-08-22 Deposition Author(s): Buts, L., Garcia-Pino, A., Wyns, L., Loris, R.
Revision History (Full details and data files)
- Version 1.0: 2006-08-22
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: 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
