5HF2

Staphylococcus aureus Dihydrofolate Reductase complexed with cyclized alpha-NADPH anomer and 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-5'-methoxy-[1,1'-biphenyl]-4-carboxylic acid (UCP1175)

PDB DOI: https://doi.org/10.2210/pdb5HF2/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-01-06 Released: 2017-01-18
Deposition Author(s): Reeve, S.M., Anderson, A.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.232
R-Value Work: 0.199
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Staphylococcus aureus Dihydrofolate Reductase complexed with cyclized alpha-NADPH anomer and 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-5'-methoxy-[1,1'-biphenyl]-4-carboxylic acid (UCP1175)

Reeve, S.M., Anderson, A.C.

To be published.

Macromolecule Content

Total Structure Weight: 19.26 kDa
Atom Count: 1,489
Modelled Residue Count: 157
Deposited Residue Count: 157
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A [auth X]	157	Staphylococcus aureus	Mutation(s): 0 Gene Names: folA EC: 1.5.1.3
UniProt
Find proteins for P0A017 (Staphylococcus aureus) Explore P0A017 Go to UniProtKB: P0A017
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A017
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XNP Query on XNP Download Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X]	B [auth X]	Tricyclic NADPH C₂₁ H₃₀ N₇ O₁₇ P₃ AJKICLDTLPZSPE-MTKBYBFRSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
U75 Query on U75 Download Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X]	C [auth X]	4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-5-methoxy-phenyl]benzoic acid C₂₃ H₂₂ N₄ O₃ VLQRVOAJCWFFQG-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth X] MOL2 format, chain D [auth X]	D [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]

Binding Affinity Annotations
ID	Source	Binding Affinity
U75	BindingDB: 5HF2	Ki: 1.6 (nM) from 1 assay(s)
U75	BindingDB: 5HF2	IC50: 11 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.232
R-Value Work: 0.199
R-Value Observed: 0.203
Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.022	α = 90
b = 79.022	β = 90
c = 108.247	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
StructureStudio	data collection

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI111957

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence
Version 1.2: 2019-12-11
Changes: Author supporting evidence
Version 1.3: 2024-03-06
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.