3EQA
Catalytic domain of glucoamylase from aspergillus niger complexed with tris and glycerol
- PDB DOI: https://doi.org/10.2210/pdb3EQA/pdb
- Classification: HYDROLASE
- Organism(s): Aspergillus niger
- Mutation(s): No
- Deposited: 2008-09-30 Released: 2009-10-13
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.229
- R-Value Work: 0.181
- R-Value Observed: 0.184
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 |
| Glucoamylase | 470 | Aspergillus niger | Mutation(s): 0 EC: 3.2.1.3 |  | |
UniProt | |||||
Find proteins for P69328 (Aspergillus niger) Explore P69328 Go to UniProtKB: P69328 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P69328 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 4 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD | |||||
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 8 |  | N-Glycosylation | |
Glycosylation Resources | |||||
GlyTouCan: G83582BK GlyCosmos: G83582BK GlyGen: G83582BK | |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MAN Query on MAN | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N |  | ||
| TRS Query on TRS | K [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| GOL Query on GOL | L [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.229
- R-Value Work: 0.181
- R-Value Observed: 0.184
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.826 | α = 90 |
| b = 73.222 | β = 90 |
| c = 106.793 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BOS | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2009-10-13 Deposition Author(s): Lee, J., Paetzel, M.
Revision History (Full details and data files)
- Version 1.0: 2009-10-13
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary
