3UPW | pdb_00003upw

Pichia Stipitis OYE2.6 complexed with nicotinamide

PDB DOI: https://doi.org/10.2210/pdb3UPW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Scheffersomyces stipitis CBS 6054
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-11-18 Released: 2012-07-11
Deposition Author(s): Pompeu, Y.A., Stewart, J.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.186 (Depositor), 0.189 (DCC)
R-Value Work:
0.158 (Depositor), 0.162 (DCC)
R-Value Observed:
0.161 (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

Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions

Pompeu, Y.A., Sullivan, B., Walton, A.Z., Stewart, J.D.

(2012) Adv Synth Catal

DOI: https://doi.org/10.1002/adsc.201200213

Macromolecule Content

Total Structure Weight: 46.28 kDa
Atom Count: 3,721
Modeled Residue Count: 404
Deposited Residue Count: 407
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Old Yellow Enzyme 2.6 (OYE2.6), NADPH dehydrogenase	A	407	Scheffersomyces stipitis CBS 6054	Mutation(s): 0 Gene Names: OYE2.6, PICST_44614 EC: 1.6.99.1
UniProt
Find proteins for A3LT82 (Scheffersomyces stipitis (strain ATCC 58785 / CBS 6054 / NBRC 10063 / NRRL Y-11545)) Explore A3LT82 Go to UniProtKB: A3LT82
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3LT82
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN 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]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NCA Query on NCA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	NICOTINAMIDE C₆ H₆ N₂ O DFPAKSUCGFBDDF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A], I [auth A], J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.186 (Depositor), 0.189 (DCC)
R-Value Work: 0.158 (Depositor), 0.162 (DCC)
R-Value Observed: 0.161 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.306	α = 90
b = 127.306	β = 90
c = 123.064	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-07-11

Deposition Author(s):

Pompeu, Y.A.

Stewart, J.D.

Revision History (Full details and data files)

Version 1.0: 2012-07-11
Type: Initial release
Version 1.1: 2015-04-29
Changes: Non-polymer description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

3UPW | pdb_00003upw

Pichia Stipitis OYE2.6 complexed with nicotinamide

Literature

Structural and Catalytic Characterization of Pichia stipitis OYE 2.6, a Useful Biocatalyst for Asymmetric Alkene Reductions

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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