2F6Q | pdb_00002f6q

The crystal structure of human peroxisomal delta3, delta2 enoyl CoA isomerase (PECI)

PDB DOI: https://doi.org/10.2210/pdb2F6Q/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-11-29 Released: 2005-12-20
Deposition Author(s): Turnbull, A., Lukacik, P., Shafqat, N., Smee, C., Berridge, G., Guo, K., von Delft, F., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A., Gileadi, O., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.257 (Depositor), 0.257 (DCC)
R-Value Work:
0.213 (Depositor), 0.215 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

The crystal structure of human peroxisomal delta3, delta2 enoyl CoA isomerase (PECI)

Turnbull, A., Lukacik, P., Shafqat, N., Smee, C., Berridge, G., Guo, K., von Delft, F., Weigelt, J., Sundstrom, M., Arrowsmith, C., Edwards, A., Gileadi, O., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 94.18 kDa
Atom Count: 5,737
Modeled Residue Count: 741
Deposited Residue Count: 840
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisomal 3,2-trans-enoyl-CoA isomerase	A, B, C	280	Homo sapiens	Mutation(s): 5 Gene Names: PECI EC: 5.3.3.8
UniProt & NIH Common Fund Data Resources
Find proteins for O75521 (Homo sapiens) Explore O75521 Go to UniProtKB: O75521
PHAROS: O75521 GTEx: ENSG00000198721
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75521
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.257 (Depositor), 0.257 (DCC)
R-Value Work: 0.213 (Depositor), 0.215 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.931	α = 90
b = 123.196	β = 90
c = 128.133	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-12-20

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2005-12-20
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary