1HF3

ATOMIC X-RAY STRUCTURE OF LIVER ALCOHOL DEHYDROGENASE CONTAINING Cadmium and a hydroxide adduct to NADH

• PDB DOI: https://doi.org/10.2210/pdb1HF3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 2000-11-27 Released: 2001-05-31 
• Deposition Author(s): Meijers, R., Morris, R.J., Adolph, H.W., Merli, A., Lamzin, V.S., Cedergen-Zeppezauer, E.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.214 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

On the Enzymatic Activation of Nadh

Meijers, R., Morris, R.J., Adolph, H.W., Merli, A., Lamzin, V.S., Cedergen-Zeppezauer, E.S.

(2001) J Biol Chem 276: 9316

• PubMed: 11134046 
• DOI: https://doi.org/10.1074/jbc.M010870200
• Primary Citation of Related Structures:  
  1HET, 1HEU, 1HF3


• PubMed Abstract: 
  

  Atomic (1 A) resolution x-ray structures of horse liver alcohol dehydrogenase in complex with NADH revealed the formation of an adduct in the active site between a metal-bound water and NADH. Furthermore, a pronounced distortion of the pyridine ring of NADH was observed. A series of quantum chemical calculations on the water-nicotinamide adduct showed that the puckering of the pyridine ring in the crystal structures can only be reproduced when the water is considered a hydroxide ion. These observations provide fundamental insight into the enzymatic activation of NADH for hydride transfer.

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Organizational Affiliation: 

European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 81.72 kDa 
• Atom Count: 6,284 
• Modelled Residue Count: 748 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALCOHOL DEHYDROGENASE E CHAIN	A, B	374	Equus caballus	Mutation(s): 0  EC: 1.1.1.1
UniProt
Find proteins for P00327 (Equus caballus) Explore P00327  Go to UniProtKB:  P00327

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], I [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MRD	F [auth A], J [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
CD	C [auth A], D [auth A], G [auth B], H [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.214 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.9	α = 90
b = 179	β = 107.5
c = 50.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-05-31 
Deposition Author(s): Meijers, R., Morris, R.J., Adolph, H.W., Merli, A., Lamzin, V.S., Cedergen-Zeppezauer, E.S.

Revision History  

• Version 1.0: 2001-05-31
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Advisory, Data collection
• Version 1.4: 2023-12-13
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description