1CDE

STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE

• PDB DOI: https://doi.org/10.2210/pdb1CDE/pdb

• Classification: TRANSFERASE(FORMYL)
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1992-05-15 Released: 1993-10-31 
• Deposition Author(s): Almassy, R.J., Janson, C.A., Kan, C.-C., Hostomska, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.250 
• R-Value Observed: 0.250 

Literature

Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase.

Almassy, R.J., Janson, C.A., Kan, C.C., Hostomska, Z.

(1992) Proc Natl Acad Sci U S A 89: 6114-6118

• PubMed: 1631098 
• DOI: https://doi.org/10.1073/pnas.89.13.6114


• PubMed Abstract: 
  

  The three-dimensional structure of phosphoribosylglycinamide formyltransferase (10-formyltetrahydrofolate:5'-phosphoribosylglycinamide formyltransferase, EC 2.1.2.2) has been solved both as an apoenzyme at 2.8-A resolution and as a ternary complex with the substrate glycinamide ribonucleotide and a folate inhibitor at 2.5-A resolution. The structure is a modified doubly wound alpha/beta sheet with flexibility in the active site, including a disordered loop in the apo structure, which is ordered in the ternary complex structure. This enzyme is a target for anti-cancer therapy and now for structure-based drug design.

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Organizational Affiliation: 

Agouron Pharmaceuticals, San Diego, CA 92121.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 95.96 kDa 
• Atom Count: 6,668 
• Modelled Residue Count: 836 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE	A, B, C, D	212	Escherichia coli	Mutation(s): 0  EC: 2.1.2.2
UniProt
Find proteins for P08179 (Escherichia coli (strain K12)) Explore P08179  Go to UniProtKB:  P08179

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DZF	F [auth A], H [auth B], J [auth C], L [auth D]	5-DEAZAFOLIC ACID C20 H20 N6 O6 NFARHPAOOHOWAL-AWEZNQCLSA-N
GAR	E [auth A], G [auth B], I [auth C], K [auth D]	GLYCINAMIDE RIBONUCLEOTIDE C7 H13 N2 O8 P OBQMLSFOUZUIOB-SHUUEZRQSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.250 
• R-Value Observed: 0.250 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.7	α = 111.5
b = 72.6	β = 82.8
c = 57	γ = 62.6

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1993-10-31 
Deposition Author(s): Almassy, R.J., Janson, C.A., Kan, C.-C., Hostomska, Z.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other