4MWS
Crystal structure of human PPCA (trigonal crystal form 1)
- PDB DOI: https://doi.org/10.2210/pdb4MWS/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): No 
- Deposited: 2013-09-25 Released: 2014-03-12 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.195 
- R-Value Work: 0.146 
- R-Value Observed: 0.149 
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 protective protein | 428 | Homo sapiens | Mutation(s): 0  Gene Names: CTSA, PPGB EC: 3.4.16.5 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P10619 (Homo sapiens) Explore P10619  Go to UniProtKB:  P10619 | |||||
PHAROS:  P10619 GTEx:  ENSG00000064601  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P10619 | ||||
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)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | C | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G17689EW GlyCosmos:  G17689EW GlyGen:  G17689EW |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | D | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G18638YB GlyCosmos:  G18638YB GlyGen:  G18638YB |
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] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | F [auth A], H [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.195 
- R-Value Work: 0.146 
- R-Value Observed: 0.149 
- Space Group: P 31 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 134.889 | α = 90 |
b = 134.889 | β = 90 |
c = 99.805 | γ = 120 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
Entry History 
Deposition Data
- Released Date: 2014-03-12  Deposition Author(s): Kolli, N., Garman, S.C.
Revision History (Full details and data files)
- Version 1.0: 2014-03-12
Type: Initial release - Version 1.1: 2015-04-15
Changes: Database references - Version 1.2: 2017-08-23
Changes: Data collection - 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: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary