2PFG | pdb_00002pfg

Crystal structure of human CBR1 in complex with BiGF2.

• PDB DOI: https://doi.org/10.2210/pdb2PFG/pdb

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


• Deposited: 2007-04-04 Released: 2007-09-25 
• Deposition Author(s): Rauh, D., Bateman, R.L., Shokat, K.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.164 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.112 (Depositor), 0.108 (DCC) 
• R-Value Observed: 
  0.115 (Depositor) 

Starting Model: experimental

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

• PubMed: 17912391 
• DOI: https://doi.org/10.1039/b707602a
• Primary Citation Related Structures: 
  2PFG


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.52 kDa 
• Atom Count: 2,690 
• Modeled Residue Count: 274 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonyl reductase [NADPH] 1	A	276	Homo sapiens	Mutation(s): 0  Gene Names: CBR1, CBR, CRN EC: 1.1.1.184 (PDB Primary Data), 1.1.1.189 (PDB Primary Data), 1.1.1.197 (PDB Primary Data), 1.1.1.196 (UniProt), 1.1.1.71 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P16152 (Homo sapiens) Explore P16152  Go to UniProtKB:  P16152
PHAROS:  P16152 GTEx:  ENSG00000159228

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
DDD	D [auth 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
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M0H	A	L-PEPTIDE LINKING	C4 H9 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.164 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.112 (Depositor), 0.108 (DCC) 
• R-Value Observed: 0.115 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.636	α = 90
b = 59.884	β = 90
c = 87.954	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Rauh, D., Bateman, R.L., Shokat, K.M.

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations