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- PDB-1l6y: Crystal Structure of Porphobilinogen Synthase Complexed with the ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1l6y | ||||||
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Title | Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid | ||||||
![]() | PORPHOBILINOGEN SYNTHASE | ||||||
![]() | LYASE / DEHYDRATASE | ||||||
Function / homology | ![]() porphobilinogen synthase / porphobilinogen synthase activity / protoporphyrinogen IX biosynthetic process / heme biosynthetic process / magnesium ion binding / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jaffe, E.K. / Kervinen, J. / Martins, J. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A. | ||||||
![]() | ![]() Title: Species-Specific Inhibition of Porphobilinogen Synthase by 4-Oxosebacic Acid Authors: Jaffe, E.K. / Kervinen, J. / Martins, J. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A. #1: ![]() Title: Mechanistic Basis for Suicide Inactivation of Porphobilinogen Synthase by 4,7-dioxosebacic acid, an Inhibitor that Shows Dramatic Species Selectivity Authors: Kervinen, J. / Jaffe, E.K. / Stauffer, F. / Neier, R. / Wlodawer, A. / Zdanov, A. | ||||||
History |
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Remark 600 | HETEROGEN Atom C4 of 4OX forms a Schiff base to NZ of Lys246. The oxygen on the C4 is eliminated ...HETEROGEN Atom C4 of 4OX forms a Schiff base to NZ of Lys246. The oxygen on the C4 is eliminated during this reaction. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.4 KB | Display | ![]() |
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PDB format | ![]() | 116.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1l6sSC 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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1 | ![]()
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Unit cell |
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Details | The biological assembly is an octamer. |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35613.727 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 442 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/4OX.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/4OX.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.17 Å3/Da / Density % sol: 70.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 3350, 10% GLYCEROL, 0.1M TRIS-HCL, PH 8.5, 0.02% SODIUM AZIDE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: Jan 18, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 92900 / Num. obs: 92714 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.9→2.03 Å / % possible all: 99.7 |
Reflection | *PLUS Lowest resolution: 40 Å / Rmerge(I) obs: 0.056 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1L6S Resolution: 1.9→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 40 Å / Rfactor obs: 0.206 / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.206 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |