8K1H

Crystal structure of ethylene glycol-bound glycerol dehydrogenase from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb8K1H/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-10 Released: 2024-05-29 
• Deposition Author(s): Kang, W.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Starting Model: experimental

Literature

Crystal 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

• DOI: https://doi.org/10.5012/jkcs.2024.68.1.32

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 39.94 kDa 
• Atom Count: 3,025 
• Modelled Residue Count: 367 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol dehydrogenase	A	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	C [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
TLA (Subject of Investigation/LOI)	E [auth A], F [auth A]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
ZN (Subject of Investigation/LOI)	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	D [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.192 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: I 4 2 2
• Diffraction Data: https://doi.org/10.18430/M38K1H

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.732	α = 90
b = 179.732	β = 90
c = 84.923	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-05-29 
Deposition Author(s): Kang, W.

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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  

• Version 1.0: 2024-05-29
  Type: Initial release