Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 22226.14 
• Atom Count: 1687 
• Residue Count: 187 
• Unique protein chains: 1

4M6J

Crystal structure of human dihydrofolate reductase (DHFR) bound to NADPH

• DOI: 10.2210/pdb4M6J/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2013-08-09 Released: 2013-09-25 
• Deposition Author(s): Bhabha, G., Ekiert, D.C., Wright, P.E., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.201 Å
• R-Value Free: 0.184 
• R-Value Work: 0.163 

Literature

Divergent evolution of protein conformational dynamics in dihydrofolate reductase.

Bhabha, G., Ekiert, D.C., Jennewein, M., Zmasek, C.M., Tuttle, L.M., Kroon, G., Dyson, H.J., Godzik, A., Wilson, I.A., Wright, P.E.

(2013) Nat.Struct.Mol.Biol. 20: 1243-1249

• PubMed: 24077226 
• DOI: 10.1038/nsmb.2676
• Primary Citation of Related Structures:  
  4M6L, 4M6K


• PubMed Abstract: 
  

Molecular evolution is driven by mutations, which may affect the fitness of an organism and are then subject to natural selection or genetic drift. Analysis of primary protein sequences and tertiary structures has yielded valuable insights into the evolution of protein function, but little is known about the evolution of functional mechanisms, protein dynamics and conformational plasticity essential for activity. We characterized the atomic-level motions across divergent members of the dihydrofolate reductase (DHFR) family. Despite structural similarity, Escherichia coli and human DHFRs use different dynamic mechanisms to perform the same function, and human DHFR cannot complement DHFR-deficient E. coli cells. Identification of the primary-sequence determinants of flexibility in DHFRs from several species allowed us to propose a likely scenario for the evolution of functionally important DHFR dynamics following a pattern of divergent evolution that is tuned by cellular environment.

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Organizational Affiliation: 

1] Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, California, USA. [2] Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California, USA. [3].

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Dihydrofolate reductase	A	187	Homo sapiens	Mutation(s): 0  Gene Names: DHFR EC: 1.5.1.3
Find proteins for P00374 (Homo sapiens) Go to Gene View: DHFR Go to UniProtKB:  P00374

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.201 Å
• R-Value Free: 0.184 
• R-Value Work: 0.163 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 38.958	α = 90.00
b = 65.525	β = 90.00
c = 152.251	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
Blu-Ice	data collection
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-09 
• Released Date: 2013-09-25 
• Deposition Author(s): Bhabha, G., Ekiert, D.C., Wright, P.E., Wilson, I.A.

Revision History 

• Version 1.0: 2013-09-25
  Type: Initial release
• Version 1.1: 2013-10-16
  Type: Database references
• Version 1.2: 2013-11-20
  Type: Database references