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- PDB-6hgn: Crystal structure of Alpha1-antichymotrypsin variant DBS-II-allo-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hgn | ||||||
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Title | Crystal structure of Alpha1-antichymotrypsin variant DBS-II-allo-L55V: an allosterically controlled doxorubicin-binding serpin with an unprecedentedly high ligand release efficacy | ||||||
![]() | (Alpha-1-antichymotrypsin) x 2 | ||||||
![]() | TRANSPORT PROTEIN / Serpin / alpha1-Antichymotrypsin / computational protein design / allosteric coupling | ||||||
Function / homology | ![]() maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle ...maintenance of gastrointestinal epithelium / regulation of lipid metabolic process / platelet alpha granule lumen / acute-phase response / serine-type endopeptidase inhibitor activity / azurophil granule lumen / Platelet degranulation / secretory granule lumen / collagen-containing extracellular matrix / blood microparticle / inflammatory response / Neutrophil degranulation / DNA binding / extracellular space / extracellular exosome / extracellular region / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schmidt, K. / Muller, Y.A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: NewBG: A surrogate corticosteroid-binding globulin with an unprecedentedly high ligand release efficacy. Authors: Gardill, B.R. / Schmidt, K. / Muller, Y.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163 KB | Display | ![]() |
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PDB format | ![]() | 130 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 457.2 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hgdC ![]() 6hgeC ![]() 6hgfC ![]() 6hggC ![]() 6hghC ![]() 6hgiC ![]() 6hgjC ![]() 6hgkC ![]() 6hglC ![]() 6hgmC ![]() 5om7S 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: 41972.488 Da / Num. of mol.: 1 Mutation: L24R, L55V, W194F,W215Y, E242Q, K244N, L269S, P270Q, K274S, W276F, R277F, D278E, A349R, V355L, K356E, I357V, T358L, L359F, L360Q Source method: isolated from a genetically manipulated source Details: - all residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density- residues following the sequence ..EVLFQ are part of ...Details: - all residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density- residues following the sequence ..EVLFQ are part of chain B, as the protein is a family member of serine proteinase inhibitors (serpins) and proteolytically cleaved between EVLFQ-GPLV Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein/peptide | Mass: 4720.580 Da / Num. of mol.: 1 / Mutation: S361G, A362P, P382D, T383N, D384F, Q386W, N387S Source method: isolated from a genetically manipulated source Details: - all residues that are present in the sample sequence but not in the PDB file could not be modelled due to missing electron density Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2 % Tacsimate pH 4.0, 0.1 M Sodium acetate trihydrate pH 4.6, 16 % w/v PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.478→42.416 Å / Num. obs: 67808 / % possible obs: 99.8 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rrim(I) all: 0.069 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.478→1.57 Å / Mean I/σ(I) obs: 1.92 / CC1/2: 0.864 / Rrim(I) all: 1.168 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5OM7 Resolution: 1.478→42.416 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.86
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.478→42.416 Å
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Refine LS restraints |
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LS refinement shell |
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