3H53
Crystal Structure of human alpha-N-acetylgalactosaminidase
- PDB DOI: https://doi.org/10.2210/pdb3H53/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): Yes 
- Deposited: 2009-04-21 Released: 2009-10-20 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.01 Å
- R-Value Free: 0.194 
- R-Value Work: 0.161 
- R-Value Observed: 0.163 
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 |
Alpha-N-acetylgalactosaminidase | 400 | Homo sapiens | Mutation(s): 1  Gene Names: NAGA EC: 3.2.1.49 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P17050 (Homo sapiens) Explore P17050  Go to UniProtKB:  P17050 | |||||
PHAROS:  P17050 GTEx:  ENSG00000198951  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P17050 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
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-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | C | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G32152BH GlyCosmos:  G32152BH GlyGen:  G32152BH |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | D, F | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | Q [auth A], X [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GOL Query on GOL | G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.01 Å
- R-Value Free: 0.194 
- R-Value Work: 0.161 
- R-Value Observed: 0.163 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 153.532 | α = 90 |
b = 114.26 | β = 96.11 |
c = 68.408 | γ = 90 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2009-10-20  Deposition Author(s): Clark, N.E., Garman, S.C.
Revision History (Full details and data files)
- Version 1.0: 2009-10-20
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - 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: 2021-10-13
Changes: Database references, Structure summary - Version 2.2: 2023-09-06
Changes: Data collection, Refinement description