4FDA | pdb_00004fda

Crystal structure of Saccharomyces cerevisiae 3-oxoacyl-[acyl-carrier-protein] reductase complexed with NADP

PDB DOI: https://doi.org/10.2210/pdb4FDA/pdb

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

Deposited: 2012-05-27 Released: 2013-08-07
Deposition Author(s): Yujie, Z., Yongxiang, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.229 (Depositor), 0.230 (DCC)
R-Value Work:
0.209 (Depositor), 0.212 (DCC)
R-Value Observed:
0.210 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of Saccharomyces cerevisiae 3-oxoacyl-[acyl-carrier-protein] reductase complexed with NADPH

Yujie, Z., Yongxiang, G.

To be published.

Macromolecule Content

Total Structure Weight: 31.45 kDa
Atom Count: 1,978
Modeled Residue Count: 243
Deposited Residue Count: 273
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-oxoacyl-[acyl-carrier-protein] reductase	A	273	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: OAR1, YKL055C EC: 1.1.1.100
UniProt
Find proteins for P35731 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35731 Go to UniProtKB: P35731
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35731
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP 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]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-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: 2.10 Å
R-Value Free: 0.229 (Depositor), 0.230 (DCC)
R-Value Work: 0.209 (Depositor), 0.212 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.73	α = 90
b = 128.73	β = 90
c = 40.65	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-08-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-08-07
Type: Initial release
Version 1.1: 2013-11-27
Changes: Structure summary
Version 1.2: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.