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pdb structures pdbqt files  (AUTODOCK GmbH)

 
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    AUTODOCK GmbH pdb structures pdbqt files
    Pdb Structures Pdbqt Files, supplied by AUTODOCK GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/pdb+structure+files/protein+pdbqt/pm39657888-117-5-8
    Average 90 stars, based on 1 article reviews
    pdb structures pdbqt files - by Bioz Stars, 2026-09
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    Article Title: The heat stability of Rhamnolipid containing egg-protein stabilised oil-in-water emulsions
    Article Snippet: The pdb structure files used in the AUTODOCK calculations were also employed in the MD simulations.



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    Primary sequence and secondary structure elements of <t>S1R.</t> ( A ) Complete primary sequence of human S1R (hS1R) is shown. Secondary structure elements—H1–H5 α helices and B1–B10 β-strands are labeled based on 5HK1 structural file (hS1R bound to PD144418) . Alpha helices in crystal structure are labeled in grey, B1-B2 β strands are labeled in yellow, and B3-B10 β-strands are labeled in red. W9 and W11 residues predicted to form cholesterol binding site are shown with a red font. The position of E102 residue mutated in ALS16 is labeled red. ( B ) Results of PSIPRED analysis of hS1R primary sequence. Ordered probability (OD) is plotted for each amino acid (open blue circles and line). Secondary structure elements from the crystal structure are shown above the OD plot. Position of E102 residue mutated in ALS16 is shown by a red circle.
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    Primary sequence and secondary structure elements of <t>S1R.</t> ( A ) Complete primary sequence of human S1R (hS1R) is shown. Secondary structure elements—H1–H5 α helices and B1–B10 β-strands are labeled based on 5HK1 structural file (hS1R bound to PD144418) . Alpha helices in crystal structure are labeled in grey, B1-B2 β strands are labeled in yellow, and B3-B10 β-strands are labeled in red. W9 and W11 residues predicted to form cholesterol binding site are shown with a red font. The position of E102 residue mutated in ALS16 is labeled red. ( B ) Results of PSIPRED analysis of hS1R primary sequence. Ordered probability (OD) is plotted for each amino acid (open blue circles and line). Secondary structure elements from the crystal structure are shown above the OD plot. Position of E102 residue mutated in ALS16 is shown by a red circle.
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    Primary sequence and secondary structure elements of <t>S1R.</t> ( A ) Complete primary sequence of human S1R (hS1R) is shown. Secondary structure elements—H1–H5 α helices and B1–B10 β-strands are labeled based on 5HK1 structural file (hS1R bound to PD144418) . Alpha helices in crystal structure are labeled in grey, B1-B2 β strands are labeled in yellow, and B3-B10 β-strands are labeled in red. W9 and W11 residues predicted to form cholesterol binding site are shown with a red font. The position of E102 residue mutated in ALS16 is labeled red. ( B ) Results of PSIPRED analysis of hS1R primary sequence. Ordered probability (OD) is plotted for each amino acid (open blue circles and line). Secondary structure elements from the crystal structure are shown above the OD plot. Position of E102 residue mutated in ALS16 is shown by a red circle.
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    Image Search Results


    Primary sequence and secondary structure elements of S1R. ( A ) Complete primary sequence of human S1R (hS1R) is shown. Secondary structure elements—H1–H5 α helices and B1–B10 β-strands are labeled based on 5HK1 structural file (hS1R bound to PD144418) . Alpha helices in crystal structure are labeled in grey, B1-B2 β strands are labeled in yellow, and B3-B10 β-strands are labeled in red. W9 and W11 residues predicted to form cholesterol binding site are shown with a red font. The position of E102 residue mutated in ALS16 is labeled red. ( B ) Results of PSIPRED analysis of hS1R primary sequence. Ordered probability (OD) is plotted for each amino acid (open blue circles and line). Secondary structure elements from the crystal structure are shown above the OD plot. Position of E102 residue mutated in ALS16 is shown by a red circle.

    Journal: International Journal of Molecular Sciences

    Article Title: Structure-Based Modeling of Sigma 1 Receptor Interactions with Ligands and Cholesterol and Implications for Its Biological Function

    doi: 10.3390/ijms241612980

    Figure Lengend Snippet: Primary sequence and secondary structure elements of S1R. ( A ) Complete primary sequence of human S1R (hS1R) is shown. Secondary structure elements—H1–H5 α helices and B1–B10 β-strands are labeled based on 5HK1 structural file (hS1R bound to PD144418) . Alpha helices in crystal structure are labeled in grey, B1-B2 β strands are labeled in yellow, and B3-B10 β-strands are labeled in red. W9 and W11 residues predicted to form cholesterol binding site are shown with a red font. The position of E102 residue mutated in ALS16 is labeled red. ( B ) Results of PSIPRED analysis of hS1R primary sequence. Ordered probability (OD) is plotted for each amino acid (open blue circles and line). Secondary structure elements from the crystal structure are shown above the OD plot. Position of E102 residue mutated in ALS16 is shown by a red circle.

    Article Snippet: To investigate the secondary structures of S1R protein, PDB files of human S1R (hS1R) and Xenopus S1R (xS1R) structures determined with X-ray diffraction (XRD) were obtained from the databank—5HK1 (hS1R bound to PD144418) [ ], 5HK2 (hS1R bound to 4-IBP) [ ], 6DK0 (hS1R bound to NE-100) [ ], 6DJZ (hS1R bound to haloperidol) [ ], 6DK1 (hS1R bound to (+)-pentazocine) [ ], 7W2F (xS1R bound to PRE084) [ ] and 7W2D (xS1R bound to S1RA) [ ].

    Techniques: Sequencing, Labeling, Binding Assay, Residue

    Structural model of S1R association with cholesterol in the membrane. ( A ) Sequence alignment of the cholesterol-binding site from SLC6A4 and tandem putative cholesterol-binding sites (CARC motifs) from S1R . The residues directly involved in interactions with cholesterol in SLC6A4 and predicted to interact with cholesterol on S1R are colored red. ( B ) Structural models of S1R with one or two cholesterol molecules bound. The residues directly involved in interactions with cholesterol in the models are colored red. Cholesterol molecules are shown by yellow. The predicted membrane boundaries are shown by the blue lines and the transparent space between the lines. ( C ) Anchored models of H1 α-helix from S1R. The models are shown for S1R in the absence of cholesterol (white), with one CHO bound (green), with two CHO bound (yellow), and for WWLL mutant (blue). The predicted membrane boundaries are shown by the blue lines and the transparent space between the lines.

    Journal: International Journal of Molecular Sciences

    Article Title: Structure-Based Modeling of Sigma 1 Receptor Interactions with Ligands and Cholesterol and Implications for Its Biological Function

    doi: 10.3390/ijms241612980

    Figure Lengend Snippet: Structural model of S1R association with cholesterol in the membrane. ( A ) Sequence alignment of the cholesterol-binding site from SLC6A4 and tandem putative cholesterol-binding sites (CARC motifs) from S1R . The residues directly involved in interactions with cholesterol in SLC6A4 and predicted to interact with cholesterol on S1R are colored red. ( B ) Structural models of S1R with one or two cholesterol molecules bound. The residues directly involved in interactions with cholesterol in the models are colored red. Cholesterol molecules are shown by yellow. The predicted membrane boundaries are shown by the blue lines and the transparent space between the lines. ( C ) Anchored models of H1 α-helix from S1R. The models are shown for S1R in the absence of cholesterol (white), with one CHO bound (green), with two CHO bound (yellow), and for WWLL mutant (blue). The predicted membrane boundaries are shown by the blue lines and the transparent space between the lines.

    Article Snippet: To investigate the secondary structures of S1R protein, PDB files of human S1R (hS1R) and Xenopus S1R (xS1R) structures determined with X-ray diffraction (XRD) were obtained from the databank—5HK1 (hS1R bound to PD144418) [ ], 5HK2 (hS1R bound to 4-IBP) [ ], 6DK0 (hS1R bound to NE-100) [ ], 6DJZ (hS1R bound to haloperidol) [ ], 6DK1 (hS1R bound to (+)-pentazocine) [ ], 7W2F (xS1R bound to PRE084) [ ] and 7W2D (xS1R bound to S1RA) [ ].

    Techniques: Membrane, Sequencing, Binding Assay, Mutagenesis

    Structural model of E102Q effects on S1R association with the membrane. ( A ) Structural models of wild type hS1R (white) and hS1R-E102Q mutant (orange) are compared. The membrane boundary is shown by the orange line. The blue arrows indicate the displacement of H4/5 and H1 α-helices in hS1R-E102Q mutant structure. ( B ) E M calculations for H1, BIND and H4/5 domains for wild type hS1R (blue circles) and hS1R-E102Q mutant (red circles).

    Journal: International Journal of Molecular Sciences

    Article Title: Structure-Based Modeling of Sigma 1 Receptor Interactions with Ligands and Cholesterol and Implications for Its Biological Function

    doi: 10.3390/ijms241612980

    Figure Lengend Snippet: Structural model of E102Q effects on S1R association with the membrane. ( A ) Structural models of wild type hS1R (white) and hS1R-E102Q mutant (orange) are compared. The membrane boundary is shown by the orange line. The blue arrows indicate the displacement of H4/5 and H1 α-helices in hS1R-E102Q mutant structure. ( B ) E M calculations for H1, BIND and H4/5 domains for wild type hS1R (blue circles) and hS1R-E102Q mutant (red circles).

    Article Snippet: To investigate the secondary structures of S1R protein, PDB files of human S1R (hS1R) and Xenopus S1R (xS1R) structures determined with X-ray diffraction (XRD) were obtained from the databank—5HK1 (hS1R bound to PD144418) [ ], 5HK2 (hS1R bound to 4-IBP) [ ], 6DK0 (hS1R bound to NE-100) [ ], 6DJZ (hS1R bound to haloperidol) [ ], 6DK1 (hS1R bound to (+)-pentazocine) [ ], 7W2F (xS1R bound to PRE084) [ ] and 7W2D (xS1R bound to S1RA) [ ].

    Techniques: Membrane, Mutagenesis

    Analysis of ligand-binding site of S1R. ( A ) Results of PSIPRED analysis of a portion of hS1R primary sequence that includes the ligand-binding site (P75–P223). Ordered probability (OD) is plotted for each amino acid (open blue circles and line). Secondary structure elements from the crystal structure shown for the corresponding region of S1R below the OD plot. Position of E102 residue mutated in ALS16 is shown by a red circle. The boundaries of regions involved in interaction with agonist (green) and antagonists (yellow) are shown by bars below the OD plot. ( B ) Overlay of fragments of the hS1R structures with 4 antagonists (all shown in yellow) from 5HK1 (hS1R bound to PD144418) , 5HK2 (hS1R receptor bound to 4-IBP) , 6DK0 (hS1R bound to NE-100) , 6DJZ (hS1R bound to haloperidol) and agonist (shown in green) 6DK1 (hS1R bound to (+)-pentazocine) . ( C ) Overlay of fragments of the xS1R structures with antagonist (shown in yellow) 7W2F (xS1R bound to PRE084) and agonist (shown in green) 7W2D (xS1R bound to S1RA) . On panels B and C, B2 β-strand is shown in orange and H4/H5 α-helices are shown in blue.

    Journal: International Journal of Molecular Sciences

    Article Title: Structure-Based Modeling of Sigma 1 Receptor Interactions with Ligands and Cholesterol and Implications for Its Biological Function

    doi: 10.3390/ijms241612980

    Figure Lengend Snippet: Analysis of ligand-binding site of S1R. ( A ) Results of PSIPRED analysis of a portion of hS1R primary sequence that includes the ligand-binding site (P75–P223). Ordered probability (OD) is plotted for each amino acid (open blue circles and line). Secondary structure elements from the crystal structure shown for the corresponding region of S1R below the OD plot. Position of E102 residue mutated in ALS16 is shown by a red circle. The boundaries of regions involved in interaction with agonist (green) and antagonists (yellow) are shown by bars below the OD plot. ( B ) Overlay of fragments of the hS1R structures with 4 antagonists (all shown in yellow) from 5HK1 (hS1R bound to PD144418) , 5HK2 (hS1R receptor bound to 4-IBP) , 6DK0 (hS1R bound to NE-100) , 6DJZ (hS1R bound to haloperidol) and agonist (shown in green) 6DK1 (hS1R bound to (+)-pentazocine) . ( C ) Overlay of fragments of the xS1R structures with antagonist (shown in yellow) 7W2F (xS1R bound to PRE084) and agonist (shown in green) 7W2D (xS1R bound to S1RA) . On panels B and C, B2 β-strand is shown in orange and H4/H5 α-helices are shown in blue.

    Article Snippet: To investigate the secondary structures of S1R protein, PDB files of human S1R (hS1R) and Xenopus S1R (xS1R) structures determined with X-ray diffraction (XRD) were obtained from the databank—5HK1 (hS1R bound to PD144418) [ ], 5HK2 (hS1R bound to 4-IBP) [ ], 6DK0 (hS1R bound to NE-100) [ ], 6DJZ (hS1R bound to haloperidol) [ ], 6DK1 (hS1R bound to (+)-pentazocine) [ ], 7W2F (xS1R bound to PRE084) [ ] and 7W2D (xS1R bound to S1RA) [ ].

    Techniques: Ligand Binding Assay, Sequencing, Residue

    Proposed conformational equilibrium of S1R. ( A ) Schematic depiction of dynamic monomer (DM) conformation and anchored monomer (AM) conformations of S1R. Possible movements of H1 α-helix (m1), H4/5 α-helices (m2) and unfolding of BIND domain (m3) are shown. The equilibrium between DM and AM conformations is affected by S1R agonists, S1R antagonists, cholesterol (CHO) in the membrane and E102Q pathogenic mutation, as shown. ( B ) Proposed distribution of different S1R conformations. AM conformation is well defined and forms a narrow peak in conformational space. DM conformation is a spectrum of molecular species that differ from each other in the tilt of H1 α-helix, position of H4/5 α-helices relative to the surface of the membrane and the folding state of BIND domain. As a result, DM conformation forms a broad peak in conformational space.

    Journal: International Journal of Molecular Sciences

    Article Title: Structure-Based Modeling of Sigma 1 Receptor Interactions with Ligands and Cholesterol and Implications for Its Biological Function

    doi: 10.3390/ijms241612980

    Figure Lengend Snippet: Proposed conformational equilibrium of S1R. ( A ) Schematic depiction of dynamic monomer (DM) conformation and anchored monomer (AM) conformations of S1R. Possible movements of H1 α-helix (m1), H4/5 α-helices (m2) and unfolding of BIND domain (m3) are shown. The equilibrium between DM and AM conformations is affected by S1R agonists, S1R antagonists, cholesterol (CHO) in the membrane and E102Q pathogenic mutation, as shown. ( B ) Proposed distribution of different S1R conformations. AM conformation is well defined and forms a narrow peak in conformational space. DM conformation is a spectrum of molecular species that differ from each other in the tilt of H1 α-helix, position of H4/5 α-helices relative to the surface of the membrane and the folding state of BIND domain. As a result, DM conformation forms a broad peak in conformational space.

    Article Snippet: To investigate the secondary structures of S1R protein, PDB files of human S1R (hS1R) and Xenopus S1R (xS1R) structures determined with X-ray diffraction (XRD) were obtained from the databank—5HK1 (hS1R bound to PD144418) [ ], 5HK2 (hS1R bound to 4-IBP) [ ], 6DK0 (hS1R bound to NE-100) [ ], 6DJZ (hS1R bound to haloperidol) [ ], 6DK1 (hS1R bound to (+)-pentazocine) [ ], 7W2F (xS1R bound to PRE084) [ ] and 7W2D (xS1R bound to S1RA) [ ].

    Techniques: Membrane, Mutagenesis

    Proposed mechanism of S1R oligomerization. ( A ) S1R in the AM monomeric form promotes the generation of large oligomers due to the formation of BIND-BIND trimers and H1-H1 dimers. Large oligomers are stabilized in the presence of cholesterol (CHO) or S1R antagonists. ( B ) S1R agonists cause the conversion of AM conformation of S1R to DM conformation resulting in a loss of BIND-BIND and H1-H1 intramolecular associations and the disassembly of large S1R oligomers and clusters.

    Journal: International Journal of Molecular Sciences

    Article Title: Structure-Based Modeling of Sigma 1 Receptor Interactions with Ligands and Cholesterol and Implications for Its Biological Function

    doi: 10.3390/ijms241612980

    Figure Lengend Snippet: Proposed mechanism of S1R oligomerization. ( A ) S1R in the AM monomeric form promotes the generation of large oligomers due to the formation of BIND-BIND trimers and H1-H1 dimers. Large oligomers are stabilized in the presence of cholesterol (CHO) or S1R antagonists. ( B ) S1R agonists cause the conversion of AM conformation of S1R to DM conformation resulting in a loss of BIND-BIND and H1-H1 intramolecular associations and the disassembly of large S1R oligomers and clusters.

    Article Snippet: To investigate the secondary structures of S1R protein, PDB files of human S1R (hS1R) and Xenopus S1R (xS1R) structures determined with X-ray diffraction (XRD) were obtained from the databank—5HK1 (hS1R bound to PD144418) [ ], 5HK2 (hS1R bound to 4-IBP) [ ], 6DK0 (hS1R bound to NE-100) [ ], 6DJZ (hS1R bound to haloperidol) [ ], 6DK1 (hS1R bound to (+)-pentazocine) [ ], 7W2F (xS1R bound to PRE084) [ ] and 7W2D (xS1R bound to S1RA) [ ].

    Techniques: