Browse by MODEL: Hybrid

SASDVX2 – Full-length SARS-CoV-2 5'ge element stem-loop 5 (5_SL5)

full stem-loop 5 of SARS-CoV-2 5'genomic end experimental SAS data
PYMOL model
Sample: Full stem-loop 5 of SARS-CoV-2 5'genomic end monomer, 48 kDa Severe acute respiratory … RNA
Buffer: 25 mM potassium phosphate, 50 mM KCl, pH: 6.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 7
Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2. J Am Chem Soc 146(44):30139-30154 (2024)
Mertinkus KR, Oxenfarth A, Richter C, Wacker A, Mata CP, Carazo JM, Schlundt A, Schwalbe H
RgGuinier 4.3 nm
Dmax 13.8 nm

SASDVY2 – Sub-element stem-loop 5a within the SARS-CoV-2 5'ge element stem-loop 5 (5_SL5)

sub-element stem-loop 5a from SARS-CoV-2 5'genomic end experimental SAS data
PYMOL model
Sample: Sub-element stem-loop 5a from SARS-CoV-2 5'genomic end monomer, 11 kDa Severe acute respiratory … RNA
Buffer: 25 mM potassium phosphate, 50 mM KCl, pH: 6.2
Experiment: SAXS data collected at EMBL P12, PETRA III on 2020 Aug 7
Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2. J Am Chem Soc 146(44):30139-30154 (2024)
Mertinkus KR, Oxenfarth A, Richter C, Wacker A, Mata CP, Carazo JM, Schlundt A, Schwalbe H
RgGuinier 1.9 nm
Dmax 6.0 nm

SASDVC3 – Sub-element stem-loop 5b within the SARS-CoV-2 5'ge element stem-loop 5 (5_SL5)

sub-element stem-loop 5b from SARS-CoV-2 5'genomic end experimental SAS data
PYMOL model
Sample: Sub-element stem-loop 5b from SARS-CoV-2 5'genomic end monomer, 8 kDa Severe acute respiratory … RNA
Buffer: 25 mM potassium phosphate, 50 mM KCl, pH: 6.2
Experiment: SAXS data collected at BM29, ESRF on 2021 Feb 3
Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2. J Am Chem Soc 146(44):30139-30154 (2024)
Mertinkus KR, Oxenfarth A, Richter C, Wacker A, Mata CP, Carazo JM, Schlundt A, Schwalbe H
RgGuinier 1.4 nm
Dmax 4.3 nm

SASDVJ6 – apo Dipeptidyl peptidase 8 (DPP8 apo)

Isoform 1 of Dipeptidyl peptidase 8 experimental SAS data
BILBOMD model
Sample: Isoform 1 of Dipeptidyl peptidase 8 dimer, 208 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2023 Oct 14
Computational study of DPP8 and DPP9: fundamental insights and inhibitor design University of Antwerp PhD thesis c:irua:209673 (2024)
Olivier Beyens, Yann Sterckx
RgGuinier 4.2 nm
Dmax 13.6 nm
VolumePorod 271 nm3

SASDVK6 – Dipeptidyl peptidase 8 (DPP8) with compound 42

Isoform 1 of Dipeptidyl peptidase 8 experimental SAS data
BILBOMD model
Sample: Isoform 1 of Dipeptidyl peptidase 8 dimer, 208 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at SWING, SOLEIL on 2023 Oct 14
Computational study of DPP8 and DPP9: fundamental insights and inhibitor design University of Antwerp PhD thesis c:irua:209673 (2024)
Olivier Beyens, Yann Sterckx
RgGuinier 4.2 nm
Dmax 13.7 nm
VolumePorod 277 nm3

SASDVL6 – apo Dipeptidyl peptidase 9 (DPP9 apo)

Isoform 1 of Dipeptidyl peptidase 9 experimental SAS data
BILBOMD model
Sample: Isoform 1 of Dipeptidyl peptidase 9 dimer, 198 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2023 Sep 23
Computational study of DPP8 and DPP9: fundamental insights and inhibitor design University of Antwerp PhD thesis c:irua:209673 (2024)
Olivier Beyens, Yann Sterckx
RgGuinier 4.2 nm
Dmax 13.3 nm
VolumePorod 290 nm3

SASDVM6 – Dipeptidyl peptidase 9 (DPP9) with compound 42

Isoform 1 of Dipeptidyl peptidase 9 experimental SAS data
BILBOMD model
Sample: Isoform 1 of Dipeptidyl peptidase 9 dimer, 198 kDa Homo sapiens protein
Buffer: 25 mM HEPES, 150 mM NaCl, 2 mM DTT, pH: 7.5
Experiment: SAXS data collected at BM29, ESRF on 2023 Sep 23
Computational study of DPP8 and DPP9: fundamental insights and inhibitor design University of Antwerp PhD thesis c:irua:209673 (2024)
Olivier Beyens, Yann Sterckx
RgGuinier 4.1 nm
Dmax 12.5 nm
VolumePorod 274 nm3

SASDS66 – Solution conformation of Harpin HrpZ2 protein from Pseudomonas syringae, a plant pathogen

Harpin Z2 experimental SAS data
CORAL model
Sample: Harpin Z2 monomer, 37 kDa Pseudomonas syringae strain … protein
Buffer: 10 mM MES, 100 mM NaF, pH: 6.2
Experiment: SAXS data collected at Rigaku BioSAXS-2000, Centre for Cellular and Molecular Biology on 2023 May 1
Solution conformation of HrpZ2 protein from Pseudomonas syringae
Arpita Goswami
RgGuinier 3.1 nm
Dmax 8.8 nm
VolumePorod 64 nm3

SASDS37 – Oligomerization initiating solution conformation of Harpin HrpZ2 protein from Pseudomonas syringae, a plant pathogen

Harpin Z2 experimental SAS data
CORAL model
Sample: Harpin Z2 monomer, 37 kDa Pseudomonas syringae strain … protein
Buffer: 10 mM MES, 100 mM NaF, pH: 6.2
Experiment: SAXS data collected at Rigaku BioSAXS-2000, Centre for Cellular and Molecular Biology on 2023 May 1
Solution conformation of HrpZ2 protein from Pseudomonas syringae
Arpita Goswami
RgGuinier 3.2 nm
Dmax 11.4 nm
VolumePorod 70 nm3

SASDU88 – SEC-SAXS of the fusion protein MPB-MabR(Rv2242) - monomeric peak

Maltose/maltodextrin-binding periplasmic protein (D108A, K109A, E198A, N199A, K265A)Uncharacterized protein Rv2242 experimental SAS data
ALPHAFOLD model
Sample: Maltose/maltodextrin-binding periplasmic protein (D108A, K109A, E198A, N199A, K265A) monomer, 40 kDa Escherichia coli (strain … protein
Uncharacterized protein Rv2242 monomer, 43 kDa Mycobacterium tuberculosis (strain … protein
Buffer: 50 mM Tris pH 7.5, 150 mM NaCl, pH:
Experiment: SAXS data collected at SWING, SOLEIL on 2024 Apr 3
Domain architecture of the Mycobacterium tuberculosis MabR (Rv2242), a member of the PucR transcription factor family Heliyon :e40494 (2024)
Megalizzi V, Tanina A, Grosse C, Mirgaux M, Legrand P, Mirandela G, Wohlkönig A, Bifani P, Wintjens R
RgGuinier 2.8 nm
Dmax 8.5 nm
VolumePorod 113 nm3