1K39

The structure of yeast delta3-delta2-enoyl-COA isomerase complexed with octanoyl-COA

PDB DOI: https://doi.org/10.2210/pdb1K39/pdb

Classification: ISOMERASE
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2001-10-02 Released: 2003-08-05
Deposition Author(s): Mursula, A.M., Geerlof, A., Hiltunen, J.K., Wierenga, R.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.29 Å
R-Value Free: 0.262
R-Value Work: 0.205
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Macromolecule Content

Total Structure Weight: 98.12 kDa
Atom Count: 6,587
Modelled Residue Count: 806
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
d3,d2-enoyl CoA isomerase ECI1	A, B, C	280	Saccharomyces cerevisiae	Mutation(s): 1 Gene Names: ECI1 EC: 5.3.3.8
UniProt
Find proteins for Q05871 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05871 Go to UniProtKB: Q05871
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05871
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CO8 Query on CO8 Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain F [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain F [auth A]	F [auth A], G [auth B], I [auth C]	OCTANOYL-COENZYME A C₂₉ H₅₀ N₇ O₁₇ P₃ S KQMZYOXOBSXMII-CECATXLMSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain I [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth C] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain D [auth A]	D [auth A], E [auth A], H [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.29 Å
R-Value Free: 0.262
R-Value Work: 0.205
R-Value Observed: 0.208
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.65	α = 90
b = 116.65	β = 90
c = 216.78	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
TRUNCATE	data reduction
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2003-08-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-08-05
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Derived calculations, Version format compliance
Version 1.3: 2018-03-07
Changes: Advisory, Data collection
Version 1.4: 2021-10-27
Changes: Advisory, Database references, Derived calculations
Version 1.5: 2023-08-16
Changes: Data collection, Refinement description

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1K39

The structure of yeast delta3-delta2-enoyl-COA isomerase complexed with octanoyl-COA

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)