7UEE

Horse liver alcohol dehydrogenase with NAD and pentafluorobenzyl alcohol at 75 K

PDB DOI: https://doi.org/10.2210/pdb7UEE/pdb

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

Deposited: 2022-03-21 Released: 2022-03-30
Deposition Author(s): Plapp, B.V., Gakhar, L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.144
R-Value Work: 0.122
R-Value Observed: 0.122

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Dependence of crystallographic atomic displacement factors on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenases

Plapp, B.V., Gakhar, L., Subramanian, R.

(2022) Acta Crystallogr D Biol Crystallogr D78: 1221-1234

DOI: https://doi.org/10.1107/S2059798322008361

Macromolecule Content

Total Structure Weight: 82.16 kDa
Atom Count: 6,981
Modelled Residue Count: 748
Deposited Residue Count: 748
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00327
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAJ (Subject of Investigation/LOI) Query on NAJ Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain L [auth B]	E [auth A], L [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE (ACIDIC FORM) C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain L [auth B]
PFB (Subject of Investigation/LOI) Query on PFB Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B]	F [auth A], M [auth B]	2,3,4,5,6-PENTAFLUOROBENZYL ALCOHOL C₇ H₃ F₅ O PGJYYCIOYBZTPU-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain M [auth B]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain N [auth B]	G [auth A], H [auth A], I [auth A], N [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	C [auth A], D [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.144
R-Value Work: 0.122
R-Value Observed: 0.122
Space Group: P 1
Diffraction Data: https://doi.org/10.15785/SBGRID/895

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.4	α = 91.72
b = 51.23	β = 103.11
c = 92.43	γ = 110.21

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
d*TREK	data scaling
O	model building
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-03-30

Deposition Author(s):

Plapp, B.V.

Gakhar, L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	AA00279
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM078446

Revision History (Full details and data files)

Version 1.0: 2022-03-30
Type: Initial release
Version 1.1: 2022-10-12
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Refinement description

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Help and Resources

7UEE

Horse liver alcohol dehydrogenase with NAD and pentafluorobenzyl alcohol at 75 K

Dependence of crystallographic atomic displacement factors on temperature (25-150 K) for complexes of horse liver alcohol dehydrogenases

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)