3JWK | pdb_00003jwk

Crystal structure of Bacillus anthracis (Y102F) dihydrofolate reductase complexed with NADPH and (S)-2,4-diamino-5-(3-methoxy-3-(3,4,5-trimethoxyphenyl)prop-1-ynyl)-6-methylpyrimidine (UCP114A)

PDB DOI: https://doi.org/10.2210/pdb3JWK/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Organism(s): Bacillus anthracis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-09-18 Released: 2010-09-29
Deposition Author(s): Anderson, A.C., Beierlein, J.M., Karri, N.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.213 (Depositor), 0.215 (DCC)
R-Value Work:
0.183 (Depositor), 0.184 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Targeted Mutations in Bacillus anthracis Dihydrofolate Reductase Condense Complex Structure-Activity Relationships

Beierlein, J.M., Karri, N.G., Anderson, A.C.

(2010) J Med Chem

Macromolecule Content

Total Structure Weight: 42.22 kDa
Atom Count: 3,178
Modeled Residue Count: 330
Deposited Residue Count: 336
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	168	Bacillus anthracis	Mutation(s): 2 Gene Names: BAS2083, BA_2237, dfrA, GBAA2237, GBAA_2237 EC: 1.5.1.3
UniProt
Find proteins for Q81R22 (Bacillus anthracis) Explore Q81R22 Go to UniProtKB: Q81R22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q81R22
Sequence Annotations Expand
Reference Sequence

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 C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
5WB Query on 5WB Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	5-[(3S)-3-methoxy-3-(3,4,5-trimethoxyphenyl)prop-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine C₁₈ H₂₂ N₄ O₄ WGUCJULKGMTPOP-CYBMUJFWSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
5WB	BindingDB: 3JWK	Ki: 9810 (nM) from 1 assay(s)
5WB	BindingDB: 3JWK	IC50: 2.91e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free: 0.213 (Depositor), 0.215 (DCC)
R-Value Work: 0.183 (Depositor), 0.184 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.858	α = 90
b = 77.858	β = 90
c = 67.526	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-09-29

Deposition Author(s):

Beierlein, J.M.

Revision History (Full details and data files)

Version 1.0: 2010-09-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2013-11-20
Changes: Non-polymer description
Version 1.3: 2021-10-13
Changes: Database references, Derived calculations
Version 1.4: 2023-09-06
Changes: Data collection, Refinement description

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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.