6V7N
Crystal Structure of a human Lysosome Resident Glycoprotein, Lysosomal Acid Lipase, and its Implications in Cholesteryl Ester Storage Disease (CESD)
- PDB DOI: https://doi.org/10.2210/pdb6V7N/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes 
- Membrane Protein: Yes  OPM
- Deposited: 2019-12-09 Released: 2020-06-17 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.62 Å
- R-Value Free: 0.222 
- R-Value Work: 0.185 
- R-Value Observed: 0.187 
wwPDB Validation   3D Report Full Report
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This is version 2.2 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 acid lipase/cholesteryl ester hydrolase | 384 | Homo sapiens | Mutation(s): 3  Gene Names: LIPA EC: 3.1.1.13 Membrane Entity: Yes  | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P38571 (Homo sapiens) Explore P38571  Go to UniProtKB:  P38571 | |||||
PHAROS:  P38571 GTEx:  ENSG00000107798  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P38571 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | E [auth A], G [auth B], H [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | F [auth A], I [auth B], J [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.62 Å
- R-Value Free: 0.222 
- R-Value Work: 0.185 
- R-Value Observed: 0.187 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 97.145 | α = 90 |
b = 165.486 | β = 90 |
c = 60.36 | γ = 90 |
Software Name | Purpose |
---|---|
BUSTER | refinement |
PDB_EXTRACT | data extraction |
HKL-3000 | data reduction |
SCALA | data scaling |
BUSTER | phasing |
Structure Validation
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Entry History 
Deposition Data
- Released Date: 2020-06-17  Deposition Author(s): Han, S.
Revision History (Full details and data files)
- Version 1.0: 2020-06-17
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2020-08-12
Changes: Database references, Structure summary - Version 2.2: 2023-10-11
Changes: Data collection, Database references, Refinement description