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 (Depositor), 0.230 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

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] mmCIF 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] mmCIF 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] mmCIF 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 (Depositor), 0.230 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

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 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.