4C4O | pdb_00004c4o

Structure of carbonyl reductase CPCR2 from Candida parapsilosis in complex with NADH

PDB DOI: https://doi.org/10.2210/pdb4C4O/pdb

Classification: OXIDOREDUCTASE
Organism(s): Candida parapsilosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-09-06 Released: 2014-07-16
Deposition Author(s): Man, H., Loderer, C., Ansorge-Schumacher, M., Grogan, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.241 (Depositor), 0.228 (DCC)
R-Value Work:
0.205 (Depositor)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of Nadh-Dependent Carbonyl Reductase (Cpcr2) from Candida Parapsilosis Provides Insight Into Mutations that Improve Catalytic Properties

Man, H., Loderer, C., Ansorge-Schumacher, M.B., Grogan, G.

(2014) ChemCatChem 6: 1103

DOI: https://doi.org/10.1002/CCTC.201300788

Macromolecule Content

Total Structure Weight: 147.63 kDa
Atom Count: 9,234
Modeled Residue Count: 1,233
Deposited Residue Count: 1,344
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONYL REDUCTASE CPCR2	A, B, C, D	336	Candida parapsilosis	Mutation(s): 0 EC: 1.1.1.1
UniProt
Find proteins for O42703 (Candida parapsilosis) Explore O42703 Go to UniProtKB: O42703
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O42703
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain R [auth C] SDF format, chain L [auth B] SDF format, chain G [auth A] MOL2 format, chain W [auth D] MOL2 format, chain R [auth C] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] mmCIF format, chain W [auth D] mmCIF format, chain R [auth C] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A]	G [auth A], L [auth B], R [auth C], W [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain R [auth C] Focus chain W [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], P [auth C], Q [auth C], U [auth D], V [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain U [auth D] Focus chain V [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A]	H [auth A] M [auth B] N [auth B] O [auth B] S [auth C] H [auth A], M [auth B], N [auth B], O [auth B], S [auth C], T [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth C] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.241 (Depositor), 0.228 (DCC)
R-Value Work: 0.205 (Depositor)
R-Value Observed: 0.207 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.72	α = 90
b = 88.84	β = 100.4
c = 118.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
BALBES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Man, H.

Loderer, C.

Ansorge-Schumacher, M.

Grogan, G.

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2015-08-19
Changes: Data collection
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description