3F0S | pdb_00003f0s

Staphylococcus aureus dihydrofolate reductase complexed with NADPH and 2,4-Diamino-5-[3-(3-methoxy-5-(3,5-dimethylphenyl)phenyl)but-1-ynyl]-6-methylpyrimidine

PDB DOI: https://doi.org/10.2210/pdb3F0S/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus RF122
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-10-25 Released: 2009-10-06
Deposition Author(s): Anderson, A.C., Frey, K.M., Liu, J., Lombardo, M.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.269 (Depositor), 0.264 (DCC)
R-Value Work:
0.201 (Depositor), 0.199 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3F0S

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystallographic Complexes of Wildtype and Mutant MRSA DHFR Reveal Interactions for Lead Design

Frey, K.M., Liu, J., Lombardo, M.N., Bolstad, D.B., Smith, A.E., Priestley, N.D., Wright, D.L., Anderson, A.C.

To be published.

Macromolecule Content

Total Structure Weight: 19.15 kDa
Atom Count: 1,350
Modeled Residue Count: 157
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trimethoprim-sensitive dihydrofolate reductase	A [auth X]	157	Staphylococcus aureus RF122	Mutation(s): 0 Gene Names: dfrB EC: 1.5.1.3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
53T Query on 53T Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	5-[(3R)-3-(5-methoxy-3',5'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine C₂₄ H₂₆ N₄ O ATFDKOLABYIYCC-INIZCTEOSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.269 (Depositor), 0.264 (DCC)
R-Value Work: 0.201 (Depositor), 0.199 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.958	α = 90
b = 78.958	β = 90
c = 107.422	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-10-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-10-06
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-11-27
Changes: Non-polymer description
Version 1.3: 2017-10-25
Changes: Refinement description
Version 1.4: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.5: 2024-04-03
Changes: Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.