Download MendeleyCrystal structure Mistletoe Lectin I from Viscum album in complex with N-acetyl-D-glucosamine at 1.94 A resolution.
Laskov, A.A., Prokofev, I.I., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.To be published.
4EB2
Crystal structure Mistletoe Lectin I from Viscum album in complex with n-acetyl-d-glucosamine at 1.94 A resolution.
- DOI: 10.2210/pdb4EB2/pdb
- Classification: HYDROLASE/SUGAR BINDING PROTEIN
- Organism(s): Viscum album
- Mutation(s): No
- Deposited: 2012-03-23 Released: 2013-03-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.94 Å
- R-Value Free: 0.226
- R-Value Work: 0.180
- R-Value Observed: 0.183
wwPDB Validation 3D Report Full Report
This is version 2.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
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(by identity cutoff) | Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Beta-galactoside-specific lectin 1 chain A | A | 249 | Viscum album | Mutation(s): 0 EC: 3.2.2.22 |  |
Find proteins for P81446 (Viscum album) Explore P81446 Go to UniProtKB: P81446 | |||||
Protein Feature ViewExpand | |||||
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(by identity cutoff) | Structure
Oligosaccharides
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
| 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 2 |  | N-Glycosylation | Oligosaccharides Interaction |
Small Molecules
| Ligands 7 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG | A, B | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | Ligand Interaction | |
| PEG Query on PEG | A, B | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | Ligand Interaction | |
| SO4 Query on SO4 | A | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | Ligand Interaction | |
| GOL Query on GOL | A, B | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| EDO Query on EDO | A, B | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| AZI Query on AZI | B | AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | A | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.94 Å
- R-Value Free: 0.226
- R-Value Work: 0.180
- R-Value Observed: 0.183
- Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 107.058 | α = 90 |
| b = 107.058 | β = 90 |
| c = 311.201 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| DNA | data collection |
| XDS | data reduction |
Entry History
Deposition Data
- Deposited Date: 2012-03-23
- Released Date: 2013-03-27 Deposition Author(s): Laskov, A.A., Prokofev, I.I., Gabdoulkhakov, A.G., Betzel, C., Mikhailov, A.M.
Revision History (Full details and data files)
- Version 1.0: 2013-03-27
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
