[English] 日本語
Yorodumi
- PDB-9oni: Crystal structure of dihydrofolate reductase (DHFR) from the fila... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9oni
TitleCrystal structure of dihydrofolate reductase (DHFR) from the filarial nematode W. bancrofti in complex with NADPH and methotrexate (MTX)
Componentsdihydrofolate reductase
KeywordsOXIDOREDUCTASE / dihydrofolate reductases / NADPH / antifolate
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
METHOTREXATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / dihydrofolate reductase
Similarity search - Component
Biological speciesWuchereria bancrofti (agent of lymphatic filariasis)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.44 Å
AuthorsFrey, K.M. / Kwarteng, S. / Goodey, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2025
Title: A virtual screening strategy to repurpose antifolate compounds as W.bancrofti DHFR inhibitors.
Authors: Kwarteng, S. / Wilhelm, J. / Salama, M. / Salama, M. / Hollander, K. / Anderson, K.S. / Goodey, N.M. / Frey, K.M.
History
DepositionMay 15, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2803
Polymers22,0821
Non-polymers1,1982
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.586, 133.586, 76.198
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-730-

HOH

21A-749-

HOH

31A-750-

HOH

-
Components

#1: Protein dihydrofolate reductase


Mass: 22082.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wuchereria bancrofti (agent of lymphatic filariasis)
Production host: Escherichia coli (E. coli) / References: UniProt: A0AAF5PZP7, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.47 Å3/Da / Density % sol: 72.5 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 100 mM trisodium citrate, pH 5.4-6.4, 25% w/v PEG4000, 200 mM ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→34.41 Å / Num. obs: 15368 / % possible obs: 86.92 % / Redundancy: 1.1 % / Biso Wilson estimate: 46.3 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.045 / Rsym value: 0.064 / Net I/σ(I): 10.77
Reflection shellResolution: 2.44→2.53 Å / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 168 / CC1/2: 0.555 / Rpim(I) all: 0.405 / Rsym value: 0.573

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.44→34.41 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 682 5.11 %Random selection
Rwork0.2255 ---
obs0.2286 13348 86.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.44→34.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1412 0 81 52 1545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051530
X-RAY DIFFRACTIONf_angle_d0.7822076
X-RAY DIFFRACTIONf_dihedral_angle_d17.921553
X-RAY DIFFRACTIONf_chiral_restr0.048221
X-RAY DIFFRACTIONf_plane_restr0.006260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.630.4094520.32061020X-RAY DIFFRACTION36
2.63-2.90.36781660.31612801X-RAY DIFFRACTION98
2.9-3.310.37571410.29072889X-RAY DIFFRACTION100
3.31-4.170.27541620.20222893X-RAY DIFFRACTION100
4.17-34.410.22941610.18693063X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more