5V4V | pdb_00005v4v

Saccharomyces cerevisiae Old Yellow Enzyme 3

PDB DOI: https://doi.org/10.2210/pdb5V4V/pdb

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

Deposited: 2017-03-10 Released: 2018-03-14
Deposition Author(s): Stewart, J.D.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.189 (Depositor), 0.192 (DCC)
R-Value Work:
0.147 (Depositor), 0.152 (DCC)
R-Value Observed:
0.150 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Saccharomyces cerevisiae Old Yellow Enzyme 3

Stewart, J.D.

To be published.

Macromolecule Content

Total Structure Weight: 91.28 kDa
Atom Count: 7,418
Modeled Residue Count: 794
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH dehydrogenase 3	A, B	400	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: OYE3, YPL171C, P2291 EC: 1.6.99.1
UniProt
Find proteins for P41816 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41816 Go to UniProtKB: P41816
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41816
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
NCA Query on NCA Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain D [auth A]	D [auth A], G [auth B]	NICOTINAMIDE C₆ H₆ N₂ O DFPAKSUCGFBDDF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.189 (Depositor), 0.192 (DCC)
R-Value Work: 0.147 (Depositor), 0.152 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.214	α = 90
b = 107.762	β = 90
c = 141.071	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1111791

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2019-11-27
Changes: Author supporting evidence
Version 1.2: 2024-03-06
Changes: Data collection, Database references

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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.