8H61 | pdb_00008h61

Ketoreductase CpKR mutant - M2

PDB DOI: https://doi.org/10.2210/pdb8H61/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candida parapsilosis
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2022-10-14 Released: 2023-10-18
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: 1.90 Å
R-Value Free:
0.216 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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: 2,928
Modeled Residue Count: 340
Deposited Residue Count: 377
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mutant M2 of ketoreductase CpKR	A [auth B]	377	Candida parapsilosis	Mutation(s): 8
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 MOL2 format, chain B mmCIF format, chain B	B	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.216 (Depositor), 0.220 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.87	α = 90
b = 77.96	β = 90
c = 84.68	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
PHASER	phasing
PHENIX	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-18

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: 2023-10-18
Type: Initial release

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.