7UDR

Horse liver alcohol dehydrogenase with NAD and pentafluorobenzyl alcohol at 25 K

• PDB DOI: https://doi.org/10.2210/pdb7UDR/pdb

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


• Deposited: 2022-03-20 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.159 
• R-Value Work: 0.124 
• R-Value Observed: 0.124 

Starting Model: experimental

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

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)

Biological Assembly Evidence: equilibrium centrifugation

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 0.159 
• R-Value Work: 0.124 
• R-Value Observed: 0.124 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.15785/SBGRID/893

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.42	α = 91.72
b = 51.21	β = 103.12
c = 92.41	γ = 110.22

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-30 
Deposition Author(s): Plapp, B.V., Gakhar, L.

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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  

• 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