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- PDB-3dz5: Human AdoMetDC with covalently bound 5'-[(2-aminooxyethyl)methyla... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3dz5 | |||||||||
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Title | Human AdoMetDC with covalently bound 5'-[(2-aminooxyethyl)methylamino]-5'-deoxy-8-methyladenosine | |||||||||
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![]() | LYASE / Complexes of AdoMetDC with 8-substituted ligands / Decarboxylase / Pyruvate / S-adenosyl-L-methionine / Spermidine biosynthesis / Zymogen / LIGASE | |||||||||
Function / homology | ![]() spermine biosynthetic process / adenosylmethionine decarboxylase / adenosylmethionine decarboxylase activity / Metabolism of polyamines / polyamine metabolic process / putrescine binding / spermidine biosynthetic process / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Bale, S. / McCloskey, D.E. / Pegg, A.E. / Secrist III, J.A. / Guida, W.C. / Ealick, S.E. | |||||||||
![]() | ![]() Title: New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C8 Substitution in Structural Analogues of S-Adenosylmethionine Authors: McCloskey, D.E. / Bale, S. / Secrist III, J.A. / Tiwari, A. / Moss III, T.H. / Valiyaveettil, J. / Brooks, W.H. / Guida, W.C. / Pegg, A.E. / Ealick, S.E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.6 KB | Display | ![]() |
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PDB format | ![]() | 56.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 763.6 KB | Display | ![]() |
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Full document | ![]() | 768.7 KB | Display | |
Data in XML | ![]() | 14.4 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3dz2C ![]() 3dz3C ![]() 3dz4C ![]() 3dz6C ![]() 3dz7C ![]() 1i7bS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 7694.577 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase |
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#2: Protein | Mass: 30685.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P17707, adenosylmethionine decarboxylase |
#3: Chemical | ChemComp-PUT / |
#4: Chemical | ChemComp-M8M / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.84 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 16% PEG 8000, 100 mM Tris, 10 mM DTT, pH 8.0, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→30 Å / Num. all: 10403 / Num. obs: 10051 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Χ2: 1.165 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.43→2.52 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 2.9 / Num. unique all: 950 / Rsym value: 0.338 / Χ2: 1.107 / % possible all: 86.8 |
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Processing
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Refinement | Starting model: 1I7B.pdb Resolution: 2.43→18.78 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 306309 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 27.513 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.27 Å2 / Biso mean: 31.596 Å2 / Biso min: 11.17 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.43→18.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.43→2.58 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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