1YXM | pdb_00001yxm

Crystal structure of peroxisomal trans 2-enoyl CoA reductase

• PDB DOI: https://doi.org/10.2210/pdb1YXM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-02-22 Released: 2005-03-15 
• Deposition Author(s): Jansson, A., Ng, S., Arrowsmith, C., Sharma, S., Edwards, A.M., Von Delft, F., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of perixomal trans 2-enoyl CoA reductase (PECRA)

Jansson, A., Ng, S., Arrowsmith, C., Sharma, S., Edwards, A.M., Von Delft, F., Sundstrom, M., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 130.94 kDa 
• Atom Count: 8,697 
• Modeled Residue Count: 1,135 
• Deposited Residue Count: 1,212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
peroxisomal trans 2-enoyl CoA reductase	A, B, C, D	303	Homo sapiens	Mutation(s): 0  Gene Names: pecr EC: 1.3.1.8 (PDB Primary Data), 1.3.1.38 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BY49 (Homo sapiens) Explore Q9BY49  Go to UniProtKB:  Q9BY49
PHAROS:  Q9BY49 GTEx:  ENSG00000115425

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	H [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N
SO4	E [auth A], G [auth B], I [auth D], J [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
PO4	F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.245 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.152	α = 90
b = 119.014	β = 90
c = 119.909	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Jansson, A., Ng, S., Arrowsmith, C., Sharma, S., Edwards, A.M., Von Delft, F., Sundstrom, M., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2005-03-15
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description