[English] 日本語
Yorodumi
- PDB-1lud: SOLUTION STRUCTURE OF DIHYDROFOLATE REDUCTASE COMPLEXED WITH TRIM... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lud
TitleSOLUTION STRUCTURE OF DIHYDROFOLATE REDUCTASE COMPLEXED WITH TRIMETHOPRIM AND NADPH, 24 STRUCTURES
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / DHFR / INHIBITOR-ENZYME COMPLEX
Function / homology
Function and homology information


response to methotrexate / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to antibiotic / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Chem-TRR / Dihydrofolate reductase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsPolshakov, V.I. / Smirnov, E.G. / Birdsall, B. / Kelly, G. / Feeney, J.
Citation
Journal: J.Biomol.Nmr / Year: 2002
Title: NMR-based solution structure of the complex of Lactobacillus casei dihydrofolate reductase with trimethoprim and NADPH
Authors: Polshakov, V.I. / Smirnov, E.G. / Birdsall, B. / Kelly, G. / Feeney, J.
#1: Journal: J.Mol.Struct. / Year: 2002
Title: Towards understanding the origins of the different specificities of binding the reduced (NADPH) and oxydised (NADP+) forms of nicotinamide adenine dinucleotide phosphate coenzyme to dihydrofolate reductase
Authors: Polshakov, V.I. / Biekofsky, R.R. / Birdsall, B. / Feeney, J.
#2: Journal: Biochemistry / Year: 1999
Title: Characterization of rates of ring-flipping in trimethoprim in its ternary complexes with Lactobacillus casei dihydrofolate reductase and coenzyme analogues
Authors: Polshakov, V.I. / Birdsall, B. / Feeney, J.
#3: Journal: Protein Sci. / Year: 1999
Title: Structure and dynamics in solution of the complex of Lactobacillus casei dihydrofolate reductase with the new lipophilic antifolate drug trimetrexate
Authors: Polshakov, V.I. / Birdsall, B. / Frenkiel, T.A. / Gargaro, A.R. / Feeney, J.
#4: Journal: J.Mol.Biol. / Year: 1998
Title: The solution structure of the complex of Lactobacillus casei dihydrofolate reductase with methotrexate
Authors: Gargaro, A.R. / Soteriou, A. / Frenkiel, T.A. / Bauer, C.J. / Birdsall, B. / Polshakov, V.I. / Barsukov, I.L. / Roberts, G.C.K. / Feeney, J.
History
DepositionMay 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2016Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3683
Polymers18,3321
Non-polymers1,0372
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 32structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

#1: Protein DIHYDROFOLATE REDUCTASE


Mass: 18331.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Plasmid: PMT702 / Production host: Escherichia coli (E. coli) / Strain (production host): NF1 / References: UniProt: P00381, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-TRR / 2,4-DIAMINO-5-(3,4,5-TRIMETHOXY-BENZYL)-PYRIMIDIN-1-IUM


Mass: 291.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N4O3 / Comment: antibiotic*YM

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1313D 15N-separated ROESY
1412D N15-rejected NOESY
1522D NOESY
162DQF-COSY
173J-MODULATED N15, H1-HSQC
184J-MODULATED N15, H1-HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
13mM DHFR-15N/TMP/NADPH, 50 mM phosphate buffer90% H2O/10% D2O
23 mM DHFR/TMP/NADPH, 50 mM phosphate buffer100% D2O
30.5mM DHFR-15N/TMP/NADPH, 50 mM phosphate buffer, 5% DMPC/DHPC (3:1)90% H2O/10% D2O
40.25mM DHFR-15N/TMP/NADPH, 50 mM phosphate buffer, 5% C12E5/hexanol90% H2O/10% D2O
Sample conditionsIonic strength: 100 mM KCl / pH: 6.5 / Pressure: ambient / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYVarianUNITY6002
Varian INOVAVarianINOVA6003

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Variancollection
NMRPipe1998-2001Delaglioprocessing
CNS0.9Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: 10 ps at 1000K, 40 ps cooling from 1000 to 0K, 1000 steps of EM
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 32 / Conformers submitted total number: 24

+
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