3WLE | pdb_00003wle

Crystal structure of (R)-carbonyl reductase from Candida Parapsilosis in complex with NAD

• PDB DOI: https://doi.org/10.2210/pdb3WLE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Candida parapsilosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-11-08 Released: 2014-07-16 
• Deposition Author(s): Wang, S.S., Nie, Y., Xu, Y., Zhang, R.Z., Huang, C.H., Chan, H.C., Guo, R.T., Xiao, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Unconserved substrate-binding sites direct the stereoselectivity of medium-chain alcohol dehydrogenase

Wang, S.S., Nie, Y., Xu, Y., Zhang, R.Z., Ko, T.P., Huang, C.H., Chan, H.C., Guo, R.T., Xiao, R.

(2014) Chem Commun (Camb) 50: 7770-7772

• PubMed: 24834985 
• DOI: https://doi.org/10.1039/c4cc01752h
• Primary Citation Related Structures: 
  3WLE, 3WLF, 3WNQ


• PubMed Abstract: 
  

  Structure-guided design of substrate-binding pocket inversed the stereoselectivity of an NADH-dependent medium-chain alcohol dehydrogenase (MDR) from Prelog to anti-Prelog. The pocket-forming amino acids, especially the unconserved residues as hotspots, play critical roles in directing MDRs' stereoselectivity.

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Organizational Affiliation: 
• School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 148.56 kDa 
• Atom Count: 11,345 
• Modeled Residue Count: 1,340 
• Deposited Residue Count: 1,364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(R)-specific carbonyl reductase	A, B, C, D	341	Candida parapsilosis	Mutation(s): 0  Gene Names: CPRADH EC: 1.1.1.1
UniProt
Find proteins for A1X808 (Candida parapsilosis) Explore A1X808  Go to UniProtKB:  A1X808

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], H [auth B], K [auth C], N [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
ZN	F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.641	α = 90
b = 106.105	β = 90
c = 145.55	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-07-16 
Deposition Author(s): Wang, S.S., Nie, Y., Xu, Y., Zhang, R.Z., Huang, C.H., Chan, H.C., Guo, R.T., Xiao, R.

Revision History  

• Version 1.0: 2014-07-16
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description