3IJ7
Directed 'in situ' Elongation as a Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic a-Amylase
- PDB DOI: https://doi.org/10.2210/pdb3IJ7/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Komagataella pastoris
- Mutation(s): No 
- Deposited: 2009-08-03 Released: 2009-10-27 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.229 
- R-Value Work: 0.193 
wwPDB Validation   3D Report Full Report
This is version 3.0 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 |
Pancreatic alpha-amylase | 496 | Homo sapiens | Mutation(s): 0  Gene Names: AMY2A EC: 3.2.1.1 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P04746 (Homo sapiens) Explore P04746  Go to UniProtKB:  P04746 | |||||
PHAROS:  P04746 GTEx:  ENSG00000243480  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04746 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CA Query on CA | D [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Modified Residues 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Type | Formula | 2D Diagram | Parent |
PCA Query on PCA | A | L-PEPTIDE LINKING | C5 H7 N O3 | GLN |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.229 
- R-Value Work: 0.193 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 52.14 | α = 90 |
b = 67.82 | β = 90 |
c = 129.92 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2009-10-27  Deposition Author(s): Li, C., Zhang, R., Withers, S.G., Brayer, G.D.
Revision History (Full details and data files)
- Version 1.0: 2009-10-27
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2018-01-24
Changes: Structure summary - Version 2.0: 2019-12-25
Changes: Data collection, Database references, Derived calculations, Polymer sequence - Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary