2PFG

Crystal structure of human CBR1 in complex with BiGF2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.112 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Glutathione traps formaldehyde by formation of a bicyclo[4.4.1]undecane adduct.

Bateman, R.Rauh, D.Shokat, K.M.

(2007) Org.Biomol.Chem. 5: 3363-3367

  • DOI: 10.1039/b707602a

  • PubMed Abstract: 
  • Glutathione forms complex reaction products with formaldehyde, which can be further modified through enzymatic modification. We studied the non-enzymatic reaction between glutathione and formaldehyde and identified a bicyclic complex containing two e ...

    Glutathione forms complex reaction products with formaldehyde, which can be further modified through enzymatic modification. We studied the non-enzymatic reaction between glutathione and formaldehyde and identified a bicyclic complex containing two equivalents of formaldehyde and one glutathione molecule by protein X-ray crystallography (PDB accession number 2PFG). We have also used (1)H, (13)C and 2D NMR spectroscopy to confirm the structure of this unusual adduct. The key feature of this adduct is the involvement of the gamma-glutamyl alpha-amine and the Cys thiol in the formation of the bicyclic ring structure. These findings suggest that the structure of GSH allows for bi-dentate masking of the reactivity of formaldehyde. As this species predominates at near physiological pH values, we suggest this adduct may have biological significance.


    Organizational Affiliation

    Howard Hughes Medical Institute, Department of Cellular and Molecular Pharmacology, UCSF, 600 16th St., San Francisco, CA 94143-2280, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carbonyl reductase [NADPH] 1
A
276Homo sapiensGene Names: CBR1 (CBR, CRN, SDR21C1)
EC: 1.1.1.197, 1.1.1.189, 1.1.1.184
Find proteins for P16152 (Homo sapiens)
Go to Gene View: CBR1
Go to UniProtKB:  P16152
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

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Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
DDD
Query on DDD

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Download CCD File 
A
(5R,10S)-5-{[(CARBOXYMETHYL)AMINO]CARBONYL}-7-OXO-3-THIA-1,6-DIAZABICYCLO[4.4.1]UNDECANE-10-CARBOXYLIC ACID
C12 H17 N3 O6 S
FNEMNSFAPZMNDP-YUMQZZPRSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M0H
Query on M0H
A
L-PEPTIDE LINKINGC4 H9 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.164 
  • R-Value Work: 0.112 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.636α = 90.00
b = 59.884β = 90.00
c = 87.954γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance