Download MendeleyCrystal Structure of Glycerol Dehydrogenase from Klebsiella pneumoniae
Ko, G.S., Nguyen, T.Q., Kho, S., Kang, W.(2024) J Korean Chem Soc 68: 32-39
8K1G
Crystal structure of ethylene glycol-bound glycerol dehydrogenase from Klebsiella pneumoniae
- PDB DOI: https://doi.org/10.2210/pdb8K1G/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Klebsiella pneumoniae
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2023-07-10 Released: 2024-05-29
- Funding Organization(s): National Research Foundation (NRF, Korea)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.207
- R-Value Work: 0.186
- R-Value Observed: 0.187
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Glycerol dehydrogenase | 367 | Klebsiella pneumoniae | Mutation(s): 0 Gene Names: gldA EC: 1.1.1.6 |  | |
UniProt | |||||
Find proteins for A6TGD6 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TGD6 Go to UniProtKB: A6TGD6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A6TGD6 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL (Subject of Investigation/LOI) Query on GOL | F [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ZN (Subject of Investigation/LOI) Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO (Subject of Investigation/LOI) Query on EDO | C [auth A], D [auth A], E [auth A], G [auth A], H [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.09 Å
- R-Value Free: 0.207
- R-Value Work: 0.186
- R-Value Observed: 0.187
- Space Group: I 4 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 182.014 | α = 90 |
| b = 182.014 | β = 90 |
| c = 80.707 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-05-29 Deposition Author(s): Kang, W.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Research Foundation (NRF, Korea) | Korea, Republic Of | 2021R1A6A1A10044154 |
| National Research Foundation (NRF, Korea) | Korea, Republic Of | 2022R1C1C1004221 |
Revision History (Full details and data files)
- Version 1.0: 2024-05-29
Type: Initial release
