4XD2 | pdb_00004xd2

Horse liver alcohol dehydrogenase-NADH complex

PDB DOI: https://doi.org/10.2210/pdb4XD2/pdb

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

Deposited: 2014-12-18 Released: 2015-01-14
Deposition Author(s): Plapp, B.V., Baskar Raj, S., Ferraro, D.J.
Funding Organization(s): National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.198 (Depositor), 0.202 (DCC)
R-Value Work:
0.177 (Depositor), 0.183 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Structure of Horse liver alcohol dehydrogenase complexed with NADH

Plapp, B.V., Baskar Raj, S., Ferraro, D.J.

To be published.

Macromolecule Content

Total Structure Weight: 81.65 kDa
Atom Count: 6,719
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
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], K [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.198 (Depositor), 0.202 (DCC)
R-Value Work: 0.177 (Depositor), 0.183 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.158	α = 92.05
b = 50.911	β = 103.05
c = 92.66	γ = 109.6

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Plapp, B.V.

Baskar Raj, S.

Ferraro, D.J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)	United States	AA00279
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM008365

Revision History (Full details and data files)

Version 1.0: 2015-01-14
Type: Initial release
Version 2.0: 2017-11-22
Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations, Source and taxonomy
Version 2.1: 2019-12-11
Changes: Author supporting evidence
Version 2.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description