Download MendeleyOligosaccharide binding of Bacillus licheniformis endo-beta-1,4-galactanase
Le Nours, J., De Maria, L., Welner, D., Jorgensen, C.T., Christensen, L.L.H., Larsen, S., Lo Leggio, L.To be published.
2GFT
Crystal structure of the E263A nucleophile mutant of Bacillus licheniformis endo-beta-1,4-galactanase in complex with galactotriose
- PDB DOI: https://doi.org/10.2210/pdb2GFT/pdb
- Classification: HYDROLASE
- Organism(s): Bacillus licheniformis
- Expression System: Bacillus subtilis
- Mutation(s): Yes
- Deposited: 2006-03-23 Released: 2006-06-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.232
- R-Value Work: 0.180
- R-Value Observed: 0.183
wwPDB Validation 3D Report Full Report
This is version 2.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glycosyl Hydrolase Family 53 | A, B | 399 | Bacillus licheniformis | Mutation(s): 1 EC: 3.2.1.89 (PDB Primary Data), 3.2.1 (UniProt) |  |
UniProt | |||||
Find proteins for Q65CX5 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65CX5 Go to UniProtKB: Q65CX5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q65CX5 | ||||
Protein Feature ViewExpand | |||||
| |||||
Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Chain Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose | C, D | 3 |  | N/A | Oligosaccharides Interaction |
Glycosylation Resources | |||||
GlyTouCan: G06996VN GlyCosmos: G06996VN GlyGen: G06996VN | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CA Query on CA | E [auth A], F [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | Ligand Interaction | |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_900114 Query on PRD_900114 | C, D | 4beta-beta-galactotriose | Oligosaccharide / Metabolism |  | Ligand Interaction |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.232
- R-Value Work: 0.180
- R-Value Observed: 0.183
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 50.273 | α = 90 |
| b = 79.354 | β = 100.56 |
| c = 103.906 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
Entry History
Deposition Data
- Released Date: 2006-06-13 Deposition Author(s): Welner, D., Le Nours, J., De Maria, L., Jorgensen, C.T., Christensen, L.L.H., Larsen, S., Lo Leggio, L.
Revision History (Full details and data files)
- Version 1.0: 2006-06-13
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: 2018-01-24
Changes: Data collection, Structure summary - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary - Version 2.1: 2021-10-20
Changes: Database references, Structure summary
