7C1E

Crystal structure of Kluyveromyces polyspora ADH (KpADH) mutant (Y127W)

• PDB DOI: https://doi.org/10.2210/pdb7C1E/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Vanderwaltozyma polyspora DSM 70294
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-05-03 Released: 2021-05-05 
• Deposition Author(s): Wu, Y.F., Zhou, J.Y., Liu, Y.F., Xu, G.C., Ni, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), National Key R&D Program of China, Natural Science Foundation of Jiangsu Province

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.183 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Starting Model: experimental

Literature

Engineering an Alcohol Dehydrogenase from Kluyveromyces polyspora for Efficient Synthesis of Ibrutinib Intermediate

Wu, Y.F., Zhou, J.Y., Ni, J., Zhu, C., Sun, Z., Xu, G.C., Ni, Y.

(2021) Adv Synth Catal 

• DOI: https://doi.org/10.1002/ADSC.202001313

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.43 kDa 
• Atom Count: 6,379 
• Modelled Residue Count: 684 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epimerase domain-containing protein	A, B	342	Vanderwaltozyma polyspora DSM 70294	Mutation(s): 1  Gene Names: Kpol_529p27
UniProt
Find proteins for A7TM80 (Vanderwaltozyma polyspora (strain ATCC 22028 / DSM 70294 / BCRC 21397 / CBS 2163 / NBRC 10782 / NRRL Y-8283 / UCD 57-17)) Explore A7TM80  Go to UniProtKB:  A7TM80

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.183 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.686	α = 90
b = 102.686	β = 90
c = 134.41	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-05-05 
Deposition Author(s): Wu, Y.F., Zhou, J.Y., Liu, Y.F., Xu, G.C., Ni, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21776112
National Key R&D Program of China	China	2018YFA0901700
Natural Science Foundation of Jiangsu Province	China	BK20171135

Revision History  

• Version 1.0: 2021-05-05
  Type: Initial release
  
• Version 1.1: 2021-11-17
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Refinement description