[English] 日本語
Yorodumi- PDB-1ia2: Candida albicans dihydrofolate reductase complexed with dihydro-n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ia2 | ||||||
---|---|---|---|---|---|---|---|
Title | Candida albicans dihydrofolate reductase complexed with dihydro-nicotinamide-adenine-dinucleotide phosphate (NADPH) and 5-[(4-METHYLPHENYL)SULFANYL]-2,4-QUINAZOLINEDIAMINE (GW578) | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / ANTIFUNGAL TARGET / REDUCTASE | ||||||
Function / homology | Function and homology information dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / DIRECT REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Whitlow, M. / Howard, A.J. / Kuyper, L.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2001 Title: X-ray Crystal Structures of Candida albicans Dihydrofolate Reductase: High Resolution Ternary Complexes in Which the Dihydronicotinamide Moiety of NADPH is Displaced by an inhibitor Authors: Whitlow, M. / Howard, A.J. / Stewart, D. / Hardman, K.D. / Chan, J.H. / Baccanari, D.P. / Tansik, R.L. / Hong, J.S. / Kuyper, L.F. #1: Journal: J.Biol.Chem. / Year: 1997 Title: X-ray Crystallographic Studies of Candida albicans Dihydrofolate Reductase. High resolution structures of the holoenzyme and an inhibited ternary complex. Authors: Whitlow, M. / Howard, A.J. / Stewart, D. / Hardman, K.D. / Kuyper, L.F. / Baccanari, D.P. / Fling, M.E. / Tansik, R.L. #2: Journal: J.Med.Chem. / Year: 1995 Title: Selective Inhibitors of Candida albicans Dihydrofolate Reductase: Activity and Selectivity of 5-(arylthio)-2,4-diaminoquinazolines Authors: Chan, J.H. / Hong, J.S. / Kuyper, L.F. / Baccanari, D.P. / Joyner, S.S. / Tansik, R.L. / Boytos, C.M. / Rudolph, S.K. #3: Journal: J.Biol.Chem. / Year: 1989 Title: Characterization of Candida Albicans Dihydrofolate Reductase Authors: Baccanari, D.P. / Tansik, R.L. / Joyner, S.S. / Fling, M.E. / Smith, P.L. / Freisheim, J.H. | ||||||
History |
| ||||||
Remark 99 | HET GROUPS NDP 193, TQ4 194, AND MES 201 ARE ASSOCIATED WITH PROTEIN CHAIN A. HET GROUPS NDP 195, ...HET GROUPS NDP 193, TQ4 194, AND MES 201 ARE ASSOCIATED WITH PROTEIN CHAIN A. HET GROUPS NDP 195, TQ4 196, AND MES 202 ARE ASSOCIATED WITH PROTEIN CHAIN B. | ||||||
Remark 600 | HETEROGEN THE INHIBITION CONSTANT (IC50) FOR 5-[(4-METHYLPHENYL) SULFANYL]-2,4-QUINAZOLINEDIAMINE ... HETEROGEN THE INHIBITION CONSTANT (IC50) FOR 5-[(4-METHYLPHENYL) SULFANYL]-2,4-QUINAZOLINEDIAMINE (GW578) IS 23 NANOMOLAR USING THE FOLLOWING ASSAY (SEE REFERENCE 0 & 3). C. ALBICANS DHFR ASSAY WAS PERFORMED IN 0.1 M IMIDAZOLE CHLORIDE BUFFER, PH 6.4, WITH 12 MM MERCAPTOETHANOL, 60 MM NADPH AND 45 MM DIHYDROFOLIC ACID IN A FINAL VOLUME OF 1 ML AT 303K. IC50 IS THE CONCENTRATION OF INHIBITOR THAT DECREASES THE VELOCITY OF THE STANDARD ASSAY BY 50%. THE ENZYME (0.2 NM), NADPH, AND VARYING CONCENTRATIONS OF INHIBITOR WERE PREINCUBATED FOR 2 MIN AT 30-C, AND THE REACTION WAS INITIATED BY THE ADDITION OF DIHYDROFOLIC ACID. STEADY STATE VELOCITIES WERE MEASURED, AND IC50 VALUES WERE CALCULATED FROM A LINEAR REGRESSION PLOT OF THE PERCENTAGE INHIBITION VS THE LOGARITHM OF THE INHIBITOR CONCENTRATION. IC50 THE PRECISION OF THE DETERMINATION IS GENERALLY ABOUT A 30%. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ia2.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ia2.ent.gz | 81.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ia2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ia2_validation.pdf.gz | 649 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ia2_full_validation.pdf.gz | 673 KB | Display | |
Data in XML | 1ia2_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 1ia2_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/1ia2 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/1ia2 | HTTPS FTP |
-Related structure data
Related structure data | 1ia1C 1ia3C 1ia4C 1ai9S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | Candida DHFR is active as a monomer. |
-Components
#1: Protein | Mass: 22194.527 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: DFR1 / Plasmid: P1869 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22906, dihydrofolate reductase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 43 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: DIHYDRO-NICOTINAMIDE-ADENINE- DINUCLEOTIDE PHOSPHATE (NADPH), 5-[(4-METHYLPHENYL) SULFANYL]-2,4-QUINAZOLINEDIAMINE (GW578), PEG-3350, POTASSIUM 4-MORPHILINEETHANESULFONIC ACID (MES), ...Details: DIHYDRO-NICOTINAMIDE-ADENINE- DINUCLEOTIDE PHOSPHATE (NADPH), 5-[(4-METHYLPHENYL) SULFANYL]-2,4-QUINAZOLINEDIAMINE (GW578), PEG-3350, POTASSIUM 4-MORPHILINEETHANESULFONIC ACID (MES), DITHIOTHREITOL (DTT). A THREE-FOLD EXCESS OF GW578 AND THREE-FOLD EXCESS OF NADPH WAS ADDED TO THE C. ALBICANS DHFR SOLUTION AND LET STAND 277K OVERNIGHT. 17-20 MG/ML C. ALBICANS DHFR IN 50 UM GW578, 50 UM NADPH, 20 MM KMES, 1 MM DTT, PH 6.5 WAS MIXED WITH AN EQUAL PART OF 26 - 34% PEG-3350, THE RESERVOIR SOLUTION. , VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418 |
Detector | Type: XENTRONICS / Detector: AREA DETECTOR / Date: Feb 22, 1989 / Details: MONOCHROMATOR |
Radiation | Monochromator: Huber graphite monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.76 Å / Num. all: 137080 / Num. obs: 35749 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.83 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.0761 / Rsym value: 0.0761 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.76→1.87 Å / Redundancy: 2.17 % / Rmerge(I) obs: 0.2983 / Mean I/σ(I) obs: 1.82 / Num. unique all: 4426 / Rsym value: 0.2983 / % possible all: 69.6 |
Reflection shell | *PLUS % possible obs: 69.6 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIRECT REPLACEMENT Starting model: CANDIDA ALBICANS DHFR (PDB ENTRY 1AI9) Resolution: 1.82→10 Å Isotropic thermal model: Konnert, J.H. & Hendrickson, W.A. (1980) Acta Crystallogr. A A36, 344. σ(F): 2 / σ(I): 0 Stereochemistry target values: Hendrickson, W.A. (1985) Methods Enzymol. 115, 252-270. Details: Restrain least-squares procedure.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|