1HET | pdb_00001het

atomic X-ray structure of liver alcohol dehydrogenase containing a hydroxide adduct to NADH

PDB DOI: https://doi.org/10.2210/pdb1HET/pdb

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

Deposited: 2000-11-25 Released: 2001-05-31
Deposition Author(s): Meijers, R., Morris, R.J., Adolph, H.W., Merli, A., Lamzin, V.S., Cedergen-Zeppezauer, E.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free:
0.135 (Depositor), 0.131 (DCC)
R-Value Work:
0.118 (Depositor)
R-Value Observed:
0.123 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Biological Chem 276: 9316

PubMed: 11134046 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M010870200
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 81.65 kDa
Atom Count: 7,694
Modeled Residue Count: 748
Deposited Residue Count: 748
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00327
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	F [auth A], J [auth B], K [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.15 Å
R-Value Free: 0.135 (Depositor), 0.131 (DCC)
R-Value Work: 0.118 (Depositor)
R-Value Observed: 0.123 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.1	α = 104.6
b = 44.4	β = 101.5
c = 94	γ = 70.5

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2001-05-31

Deposition Author(s):

Cedergen-Zeppezauer, E.S.

Revision History (Full details and data files)

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: Data collection
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description