7C1E | pdb_00007c1e

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.183 (Depositor), 0.187 (DCC)
R-Value Work:
0.153 (Depositor), 0.161 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

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

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A7TM80
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.183 (Depositor), 0.187 (DCC)
R-Value Work: 0.153 (Depositor), 0.161 (DCC)
R-Value Observed: 0.154 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-05

Deposition Author(s):

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.