6UHX | pdb_00006uhx

Crystal structure of YIR035C short chain dehydrogenases/reductase from Saccharomyces cerevisiae

PDB DOI: https://doi.org/10.2210/pdb6UHX/pdb

Classification: OXIDOREDUCTASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-09-29 Released: 2020-08-05
Deposition Author(s): Stogios, P.J., Skarina, T., Chen, C., Kagan, O., Iakounine, A., Savchenko, A.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.315 (Depositor), 0.320 (DCC)
R-Value Work:
0.235 (Depositor), 0.240 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of YIR035C short chain dehydrogenases/reductase from Saccharomyces cerevisiae

Chen, C.

To be published.

Macromolecule Content

Total Structure Weight: 56.5 kDa
Atom Count: 4,058
Modeled Residue Count: 507
Deposited Residue Count: 508
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized oxidoreductase YIR035C	A, B	254	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: YIR035C EC: 1 (PDB Primary Data), 1.1.1.320 (UniProt)
UniProt
Find proteins for P40579 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40579 Go to UniProtKB: P40579
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40579
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP (Subject of Investigation/LOI) Query on NAP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.315 (Depositor), 0.320 (DCC)
R-Value Work: 0.235 (Depositor), 0.240 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.545	α = 90
b = 73.049	β = 100.137
c = 67.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
Coot	model building
PHENIX	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	Industrial Biocatalysis Network

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, 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.