7Y0K

Crystal structure of CpKR in complex with NADPH complex from Candida parapsilosis

PDB DOI: https://doi.org/10.2210/pdb7Y0K/pdb

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

Deposited: 2022-06-05 Released: 2023-06-14
Deposition Author(s): Chen, C., Pan, J., Xu, J.H.
Funding Organization(s): National Key Research and Development Program of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free: 0.268
R-Value Work: 0.200
R-Value Observed: 0.204

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Computational Redesign of a robust Ketoreductase for Asymmetric Synthesis of Enantiopure diltiazem precursor.

Chen, C., Pan, J., Xu, J.H.

To be published.

Macromolecule Content

Total Structure Weight: 42.24 kDa
Atom Count: 2,617
Modelled Residue Count: 329
Deposited Residue Count: 377
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epimerase domain-containing protein	A	377	Candida parapsilosis	Mutation(s): 0 Gene Names: CPAR2_100480
UniProt
Find proteins for G8B6C8 (Candida parapsilosis (strain CDC 317 / ATCC MYA-4646)) Explore G8B6C8 Go to UniProtKB: G8B6C8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G8B6C8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP (Subject of Investigation/LOI) Query on NDP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.03 Å
R-Value Free: 0.268
R-Value Work: 0.200
R-Value Observed: 0.204
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.046	α = 67.44
b = 45.454	β = 84.88
c = 48.921	γ = 68.28

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Key Research and Development Program of China	China	2019YFA09005000

Revision History (Full details and data files)

Version 1.0: 2023-06-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.