2OHX | pdb_00002ohx

REFINED CRYSTAL STRUCTURE OF LIVER ALCOHOL DEHYDROGENASE-NADH COMPLEX AT 1.8 ANGSTROMS RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2OHX/pdb

• Classification: OXIDOREDUCTASE(NAD(A)-CHOH(D))
• Organism(s): Equus caballus
• Mutation(s): No 


• Deposited: 1993-08-24 Released: 1993-10-31 
• Deposition Author(s): Al-Karadaghi, S., Cedergren-Zeppezauer, E.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Refined crystal structure of liver alcohol dehydrogenase-NADH complex at 1.8 A resolution.

Al-Karadaghi, S., Cedergren-Zeppezauer, E.S., Hovmoller, S.

(1994) Acta Crystallogr D Biol Crystallogr 50: 793-807

• PubMed: 15299346 
• DOI: https://doi.org/10.1107/S0907444994005263
• Primary Citation Related Structures: 
  2OHX


• PubMed Abstract: 
  

  The crystal structure of the ternary complex of horse liver alcohol dehydrogenase (LADH) with the coenzyme NADH and inhibitor dimethyl sulfoxide (DMSO) has been refined by simulated annealing with molecular dynamics and restrained positional refinement using the program X-PLOR. The two subunits of the enzyme were refined independently. The space group was P1 with cell dimensions a = 51.8, b = 44.5, c = 94.6 A, alpha = 104.8, beta = 102.3 and gamma = 70.6 degrees. The resulting crystallographic R factor is 17.3% for 62 440 unique reflections in the resolution range 10.0-1.8 A. A total of 472 ordered solvent molecules were localized in the structure. An analysis of secondary-structure elements, solvent content and NADH binding is presented.

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Organizational Affiliation: 
• Department of Structural Chemistry, Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 81.45 kDa 
• Atom Count: 6,129 
• Modeled Residue Count: 748 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALCOHOL DEHYDROGENASE	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
DMS	F [auth A], J [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.76	α = 104.8
b = 44.54	β = 102.3
c = 94.61	γ = 70.6

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Al-Karadaghi, S., Cedergren-Zeppezauer, E.S.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Advisory, Derived calculations, Other
• Version 1.4: 2024-02-21
  Changes: Advisory, Data collection, Database references, Derived calculations