7Y0K | pdb_00007y0k

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 (Depositor), 0.271 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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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
Modeled Residue Count: 329
Deposited Residue Count: 377
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.271 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.204 (Depositor)

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

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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

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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.