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Open data
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Basic information
Entry | Database: PDB / ID: 6dag | ||||||
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Title | Human CYP3A4 bound to an inhibitor | ||||||
![]() | Cytochrome P450 3A4![]() | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sevrioukova, I.F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-Activity Relationships of Rationally Designed Ritonavir Analogues: Impact of Side-Group Stereochemistry, Headgroup Spacing, and Backbone Composition on the Interaction with CYP3A4. Authors: Samuels, E.R. / Sevrioukova, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 208.3 KB | Display | ![]() |
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PDB format | ![]() | 165.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6da2C ![]() 6da3C ![]() 6da5C ![]() 6da8C ![]() 6daaC ![]() 6dabC ![]() 6dacC ![]() 6dajC ![]() 6dalC ![]() 5vccS 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: 55757.812 Da / Num. of mol.: 1 / Fragment: residues 23-503 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: P08684, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: P08684, ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HEM / ![]() |
#3: Chemical | ChemComp-G0Y / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.4 % |
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Crystal grow![]() | Temperature: 293 K / Method: microbatch / Details: PEG 3350, sodium malonate |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 19, 2017 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.8→79.33 Å / Num. obs: 11551 / % possible obs: 93.1 % / Redundancy: 3.3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.06 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3 % / Rmerge(I) obs: 2.668 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 1645 / CC1/2: 0.317 / Rpim(I) all: 1.698 / % possible all: 93.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5VCC Resolution: 2.8→51.175 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 39.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→51.175 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -19.3439 Å / Origin y: -27.339 Å / Origin z: -12.6636 Å
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Refinement TLS group | Selection details: all |