3WEZ
Crystal structure of human beta-galactosidase in complex with NOEV
- PDB DOI: https://doi.org/10.2210/pdb3WEZ/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Komagataella pastoris
- Mutation(s): No 
- Deposited: 2013-07-16 Released: 2014-04-23 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.11 Å
- R-Value Free: 0.225 
- R-Value Work: 0.179 
- R-Value Observed: 0.181 
This is version 1.2 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 |
Beta-galactosidase | 678 | Homo sapiens | Mutation(s): 0  Gene Names: ELNR1, GLB1 EC: 3.2.1.23 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P16278 (Homo sapiens) Explore P16278  Go to UniProtKB:  P16278 | |||||
PHAROS:  P16278 GTEx:  ENSG00000170266  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P16278 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
N8V Query on N8V | DA [auth C], J [auth A], NA [auth D], T [auth B] | (1S,2S,3S,6R)-4-(hydroxymethyl)-6-(octylamino)cyclohex-4-ene-1,2,3-triol C15 H29 N O4 UPZUHYMBTUUPML-QPSCCSFWSA-N | |||
NAG Query on NAG | AA [auth C] BA [auth C] E [auth A] F [auth A] G [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
SO4 Query on SO4 | EA [auth C] FA [auth C] K [auth A] L [auth A] OA [auth D] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
EDO Query on EDO | GA [auth C] HA [auth C] M [auth A] N [auth A] QA [auth D] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
CL Query on CL | CA [auth C], I [auth A], MA [auth D], S [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.11 Å
- R-Value Free: 0.225 
- R-Value Work: 0.179 
- R-Value Observed: 0.181 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 94.933 | α = 90 |
b = 115.915 | β = 92.25 |
c = 140.51 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2014-04-23  Deposition Author(s): Suzuki, H., Ohto, U., Shimizu, T.
Revision History (Full details and data files)
- Version 1.0: 2014-04-23
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary