5KZX
Crystal structure of human GAA
- PDB DOI: https://doi.org/10.2210/pdb5KZX/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): No 
- Deposited: 2016-07-25 Released: 2017-07-26 
- Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.185 
- R-Value Work: 0.154 
- R-Value Observed: 0.156 
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 |
Lysosomal alpha-glucosidase | 874 | Homo sapiens | Mutation(s): 0  Gene Names: GAA EC: 3.2.1.20 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P10253 (Homo sapiens) Explore P10253  Go to UniProtKB:  P10253 | |||||
PHAROS:  P10253 GTEx:  ENSG00000171298  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P10253 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | B | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G38216KS GlyCosmos:  G38216KS |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C, D | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
BGC Query on BGC | I [auth A], K [auth A] | beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N | |||
GLC Query on GLC | H [auth A], J [auth A] | alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N | |||
PGE Query on PGE | N [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N | |||
PEG Query on PEG | O [auth A], R [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
SO4 Query on SO4 | P [auth A], Q [auth A], S [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
EDO Query on EDO | L [auth A], M [auth A], T [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.185 
- R-Value Work: 0.154 
- R-Value Observed: 0.156 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 97.11 | α = 90 |
b = 102.59 | β = 90 |
c = 128.55 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
Aimless | data scaling |
PDB_EXTRACT | data extraction |
iMOSFLM | data reduction |
AMoRE | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-07-26  Deposition Author(s): Deming, D.T., Garman, S.C.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) | United States | -- |
Revision History (Full details and data files)
- Version 1.0: 2017-07-26
Type: Initial release - Version 1.1: 2018-01-17
Changes: Author supporting evidence - Version 1.2: 2019-12-04
Changes: Author supporting evidence, Data collection - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary - Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary