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- PDB-1dia: HUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE CO... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1dia | ||||||
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Title | HUMAN METHYLENETETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE COMPLEXED WITH NADP AND INHIBITOR LY249543 | ||||||
![]() | METHYLENETETRAHYDROFOLATE DEHYDROGENASE/CYCLOHYDROLASE | ||||||
![]() | OXIDOREDUCTASE / HYDROLASE / TETRAHYDROFOLATE / DEHYDROGENASE / CYCLOHYDROLASE / NADP / INHIBITOR / ROSSMANN FOLD | ||||||
Function / homology | ![]() methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity / serine family amino acid biosynthetic process / 10-formyltetrahydrofolate biosynthetic process / purine ribonucleotide biosynthetic process / serine family amino acid metabolic process / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / methylenetetrahydrofolate dehydrogenase (NADP+) / embryonic neurocranium morphogenesis ...methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity / serine family amino acid biosynthetic process / 10-formyltetrahydrofolate biosynthetic process / purine ribonucleotide biosynthetic process / serine family amino acid metabolic process / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / methylenetetrahydrofolate dehydrogenase (NADP+) / embryonic neurocranium morphogenesis / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / embryonic viscerocranium morphogenesis / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine metabolic process / somite development / Metabolism of folate and pterines / methionine biosynthetic process / transsulfuration / neutrophil homeostasis / purine nucleotide biosynthetic process / tetrahydrofolate interconversion / neural tube closure / one-carbon metabolic process / heart development / mitochondrion / extracellular exosome / ATP binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Schmidt, A. / Wu, H. / MacKenzie, R.E. / Chen, V.J. / Bewly, J.R. / Ray, J.E. / Toth, J.E. / Cygler, M. | ||||||
![]() | ![]() Title: Structures of three inhibitor complexes provide insight into the reaction mechanism of the human methylenetetrahydrofolate dehydrogenase/cyclohydrolase. Authors: Schmidt, A. / Wu, H. / MacKenzie, R.E. / Chen, V.J. / Bewly, J.R. / Ray, J.E. / Toth, J.E. / Cygler, M. #1: ![]() Title: The 3-D Structure of a Folate-Dependent Dehydrogenase/Cyclohydrolase Bifunctional Enzyme at 1.5 A Resolution Authors: Allaire, M. / Li, Y. / MacKenzie, R.E. / Cygler, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.5 KB | Display | ![]() |
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PDB format | ![]() | 97.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 35 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | DC301 forms dimers, the two monomers (chains A and B) being related by a noncrystallographic twofold axis in the crystal structure. |
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Components
#1: Protein | Mass: 33338.418 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11586, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase #2: Chemical | #3: Chemical | ChemComp-L24 / [[[ | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.49 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG 3350, GLYCEROL, SODIUM CITRATE, AMMONIUM ACETATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 20K | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: protein/inhibitor ratio is 1:100 | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→15 Å / Num. all: 29674 / Num. obs: 29674 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.2→2.23 Å / Redundancy: 4 % / Rmerge(I) obs: 0.146 / % possible all: 95.5 |
Reflection | *PLUS Num. obs: 29512 / Num. measured all: 175474 |
Reflection shell | *PLUS % possible obs: 95.5 % |
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Processing
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Refinement | Resolution: 2.2→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT CORRECTION APPLIED
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Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 28962 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |