1CDD | pdb_00001cdd

STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE

• PDB DOI: https://doi.org/10.2210/pdb1CDD/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: 2.80 Å
• R-Value Work: 
  0.210 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

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
• Primary Citation of Related Structures:  
  1CDD, 1CDE


• 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.72 kDa 
• Atom Count: 2,918 
• Modeled Residue Count: 378 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE	A, B	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Work:  0.210 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.9	α = 90
b = 97.6	β = 90
c = 102.4	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
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