Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25000.71 
• Atom Count: 1772 
• Residue Count: 205 
• Unique protein chains: 1

1VJ3

STRUCTURAL STUDIES ON BIO-ACTIVE COMPOUNDS. CRYSTAL STRUCTURE AND MOLECULAR MODELING STUDIES ON THE PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COFACTOR COMPLEX WITH TAB, A HIGHLY SELECTIVE ANTIFOLATE.

• DOI: 10.2210/pdb1VJ3/pdb
• Entry 1VJ3 supersedes 1D8R

• Classification: OXIDOREDUCTASE
• Organism(s): Pneumocystis carinii
• Expression System: Escherichia coli


• Deposited: 2004-01-13 Released: 2004-01-20 
• Deposition Author(s): Cody, V., Galitsky, N., Rak, D., Luft, J.R., Queener, S.F., Laughton, C.A., Malcolm, F.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å

Literature

Structural studies on bioactive compounds. 30. Crystal structure and molecular modeling studies on the Pneumocystis carinii dihydrofolate reductase cofactor complex with TAB, a highly selective antifolate.

Cody, V., Chan, D., Galitsky, N., Rak, D., Luft, J.R., Pangborn, W., Queener, S.F., Laughton, C.A., Stevens, M.F.

(2000) Biochemistry 39: 3556-3564

• PubMed: 10736154 
• Primary Citation of Related Structures:  
  1D8R


• PubMed Abstract: 
  

The crystal structure of the ternary complex of NADPH, the potent antifolate [2, 4-diamino-5-¿3-[3-(2-acetyloxyethyl)-3-benzyltriazen-1-yl]-4 -chloroph enyl¿-6-ethylpyrimidine] (TAB, 1) and Pneumocystis carinii dihydrofolate reductase (pcDHFR), refined to 2.1 A resolution, reveals that TAB binds similar to the antifolates trimethoprim and methotrexate. These data also reveal multiple conformations for the binding geometry of TAB with two preferred orientations of the acetyloxy and benzyl groups that results from a 180 degrees rotation about the N2-N3 triazenyl bond. The methyl of the acetyloxy and benzyl ring of TAB probes large hydrophobic regions of the p-aminobenzoyl folate binding pocket of the active site, in particular the region near Phe69, which is unique to the pcDHFR sequence. These results confirm prior molecular modeling investigations of the binding of TAB to pcDHFR that identified four low-energy binding geometries, two involving rotations about the terminal N(2)-N(3) triazenyl linkage and two involving atropisomerism about the pivotal pyrimethamine-phenyl bond. The primary differences in the molecular dynamics (MD) models and those observed in this crystal complex result from small conformational changes in active-site residues on energy minimization. However, two MD models place the acetyloxy and benzyl ring groups in a region of the active site between the cofactor-binding region and the p-aminobenzoyl folate pocket; an orientation never observed in any DHFR crystal structure to date. These conformers interact with solvent near the enzyme surface and are probably not observed due to the loss of specific hydrogen bonds with the enzyme. The high species pcDHFR selectivity of TAB could be the result of ligand flexibility that enables multiple binding orientations at the enzyme active site. Further modification of the acetyloxy region of TAB could increase its potency and selectivity for pcDHFR.

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Related Citations: 

• Ligand-Induced Conformational Changes in the Crystal Structures of Pneumocystis Carinii Dihydrofolate Reductase Complexes with Folate and Nadp+
  Cody, V.,Galitsky, N.,Rak, D.,Luft, J.R.,Pangborn, W.,Queener, S.F.
  (1999) Biochemistry 38: 4303
• The Structure of Pneumocystis Carinii Dihydrofolate Reductase to 1.9 A Resolution
  Champness, J.N.,Achari, A.,Ballantine, S.P.,Bryant, P.K.,Delves, C.J.,Stammers, D.K.
  (1994) Structure 2: 915




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Organizational Affiliation: 

Hauptman-Woodward Medical Research Institute, Inc., Buffalo, New York 14203, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DIHYDROFOLATE REDUCTASE	A	205	Pneumocystis carinii	Mutation(s): 0  EC: 1.5.1.3
Find proteins for P16184 (Pneumocystis carinii) Go to UniProtKB:  P16184

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NDP	A	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
TAB	A	ACETIC ACID N-[2-CHLORO-5-[6-ETHYL-2,4-DIAMINO-PYRIMID-5-YL]-PHENYL]-[BENZYL-TRIAZEN-3-YL]ETHYL ESTER C23 H26 Cl N7 O2 QKBISNUGIKKCIM-QVIHXGFCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TAB	IC50: 170 nM (100) BINDINGDB
TAB	IC50: 170 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 37.481	α = 90.00
b = 43.137	β = 94.74
c = 61.288	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
AMoRE	phasing
PROFFT	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-01-13 
• Released Date: 2004-01-20 
• Deposition Author(s): Cody, V., Galitsky, N., Rak, D., Luft, J.R., Queener, S.F., Laughton, C.A., Malcolm, F.G.
• This entry supersedes: 1D8R

Revision History 

• Version 1.0: 2004-01-20
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-04
  Type: Refinement description