5HF0 | pdb_00005hf0

Staphylococcus aureus Dihydrofolate Reductase complexed with beta-NADPH, cyclic alpha-NADPH anomer and 3'-(3-(2,4-diamino-6-ethylpyrimidin-5-yl)prop-2-yn-1-yl)-4'-methoxy-[1,1'-biphenyl]-4-carboxylic acid (UCP1106)

PDB DOI: https://doi.org/10.2210/pdb5HF0/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): Anderson, A.C., Reeve, S.M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free:
0.217 (Depositor), 0.220 (DCC)
R-Value Work:
0.168 (Depositor), 0.179 (DCC)
R-Value Observed:
0.170 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5HF0

Ligand Structure Quality Assessment

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

Literature

Staphylococcus aureus Dihydrofolate Reductase complexed with NADPH and 6-ETHYL-5-[(3S)-3-[3-METHOXY-5-(PYRIDIN-4-YL)PHENYL]BUT-1-YN-1-YL]PYRIMIDINE-2,4-DIAMINE (UCP1106)

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

To be published.

Macromolecule Content

Total Structure Weight: 20.38 kDa
Atom Count: 1,498
Modeled Residue Count: 157
Deposited Residue Count: 160
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A [auth X]	160	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A017
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XNP Query on XNP 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]	Tricyclic NADPH C₂₁ H₃₀ N₇ O₁₇ P₃ AJKICLDTLPZSPE-MTKBYBFRSA-N		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain E [auth X] MOL2 format, chain E [auth X] mmCIF format, chain E [auth X]	E [auth X]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth X] Interactions & Density Focus chain E [auth X]
U06 Query on U06 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]-4-methoxy-phenyl]benzoic acid C₂₃ H₂₂ N₄ O₃ KQGRJTMRAQWNLV-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 B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 Å
R-Value Free: 0.217 (Depositor), 0.220 (DCC)
R-Value Work: 0.168 (Depositor), 0.179 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.098	α = 90
b = 79.098	β = 90
c = 107.931	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

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

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