SASBDB entries for UniProt ID:

SASDLK2 – Pro-CPG2-3 (pro-enzyme design 3 of circular permutant Carboxypeptidase G2-CP-N89-K177A)

UniProt ID: P06621 (89-415) Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 3
Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 3 experimental SAS data
ROSETTA model
Sample: Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 3 dimer, 100 kDa Pseudomonas sp. (strain … protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.4
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 8
Massively parallel, computationally guided design of a proenzyme. Proc Natl Acad Sci U S A 119(15):e2116097119 (2022)
Yachnin BJ, Azouz LR, White RE 3rd, Minetti CASA, Remeta DP, Tan VM, Drake JM, Khare SD
RgGuinier 3.7 nm
Dmax 13.0 nm
VolumePorod 127 nm3

SASDLL2 – Pro-CPG2-3 (pro-enzyme design 3 of circular permutant Carboxypeptidase G2-CP-N89-K177A) with Methotrexate

UniProt ID: None (None-None) Methotrexate

UniProt ID: P06621 (89-415) Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 3
MethotrexatePro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 3 experimental SAS data
ROSETTA model
Sample: Methotrexate dimer, 1 kDa
Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 3 dimer, 100 kDa Pseudomonas sp. (strain … protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.4
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 May 8
Massively parallel, computationally guided design of a proenzyme. Proc Natl Acad Sci U S A 119(15):e2116097119 (2022)
Yachnin BJ, Azouz LR, White RE 3rd, Minetti CASA, Remeta DP, Tan VM, Drake JM, Khare SD
RgGuinier 3.5 nm
Dmax 12.3 nm
VolumePorod 125 nm3

SASDLM2 – Pro-CPG2-1-Disulfide (pro-enzyme design 1 disulfide variant of circular permutant Carboxypeptidase G2-CP-N89-K177A)

UniProt ID: P06621 (89-415) Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 1 Disulfide Variant
Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 1 Disulfide Variant experimental SAS data
ROSETTA model
Sample: Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 1 Disulfide Variant dimer, 96 kDa Pseudomonas sp. (strain … protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.4
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Dec 6
Massively parallel, computationally guided design of a proenzyme. Proc Natl Acad Sci U S A 119(15):e2116097119 (2022)
Yachnin BJ, Azouz LR, White RE 3rd, Minetti CASA, Remeta DP, Tan VM, Drake JM, Khare SD
RgGuinier 3.6 nm
Dmax 12.6 nm
VolumePorod 120 nm3

SASDLN2 – Pro-CPG2-1-Disulfide (pro-enzyme design 1 disulfide variant of circular permutant Carboxypeptidase G2-CP-N89-K177A) with Methotrexate

UniProt ID: None (None-None) Methotrexate

UniProt ID: P06621 (89-415) Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 1 Disulfide Variant
MethotrexatePro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 1 Disulfide Variant experimental SAS data
ROSETTA model
Sample: Methotrexate dimer, 1 kDa
Pro-Carboxypeptidase G2 (circular permutant CP-N89) K177A Design 1 Disulfide Variant dimer, 96 kDa Pseudomonas sp. (strain … protein
Buffer: 50 mM Tris, 100 mM NaCl, pH: 7.4
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Dec 6
Massively parallel, computationally guided design of a proenzyme. Proc Natl Acad Sci U S A 119(15):e2116097119 (2022)
Yachnin BJ, Azouz LR, White RE 3rd, Minetti CASA, Remeta DP, Tan VM, Drake JM, Khare SD
RgGuinier 3.5 nm
Dmax 12.3 nm
VolumePorod 125 nm3

SASDLP2 – Outer membrane associated protein, FopA dimer in Tris-HCl, NaCl and n-Dodecyl beta-D-maltoside

UniProt ID: Q5NH85 (24-393) Francisella tularensis outer membrane protein A
Francisella tularensis outer membrane protein A experimental SAS data
Sample: Francisella tularensis outer membrane protein A dimer, 80 kDa Francisella tularensis subsp. … protein
Buffer: 20 mM Tris, 150 mM NaCl, 0.05% B-DDM, pH: 7.5
Experiment: SAXS data collected at BioCAT 18ID, Advanced Photon Source (APS), Argonne National Laboratory on 2019 Mar 20
Structural and biophysical properties of FopA, a major outer membrane protein of Francisella tularensis. PLoS One 17(8):e0267370 (2022)
Nagaratnam N, Martin-Garcia JM, Yang JH, Goode MR, Ketawala G, Craciunescu FM, Zook JD, Sonowal M, Williams D, Grant TD, Fromme R, Hansen DT, Fromme P
RgGuinier 4.4 nm
Dmax 16.0 nm
VolumePorod 330 nm3

SASDLQ2 – PfMDH L-lactate dehydrogenase, apo

UniProt ID: Q6VVP7 (1-313) L-lactate dehydrogenase
L-lactate dehydrogenase experimental SAS data
PYMOL model
Sample: L-lactate dehydrogenase tetramer, 141 kDa Plasmodium falciparum protein
Buffer: 100 mM Na-phosphate buffer, 400 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss 2.0 with MetalJet, Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University on 2019 Jul 3
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity Communications Biology 4(1) (2021)
Reyes Romero A, Lunev S, Popowicz G, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak T, Dömling A, Groves M
RgGuinier 3.4 nm
Dmax 10.5 nm
VolumePorod 211 nm3

SASDLR2 – PfMDH L-lactate dehydrogenase bound to inhibitor 2a

UniProt ID: Q6VVP7 (1-313) L-lactate dehydrogenase
L-lactate dehydrogenase experimental SAS data
DAMMIF model
Sample: L-lactate dehydrogenase tetramer, 141 kDa Plasmodium falciparum protein
Buffer: 100 mM Na-phosphate buffer, 400 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss 2.0 with MetalJet, Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University on 2019 Jul 3
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity Communications Biology 4(1) (2021)
Reyes Romero A, Lunev S, Popowicz G, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak T, Dömling A, Groves M
RgGuinier 3.4 nm
Dmax 10.5 nm
VolumePorod 244 nm3

SASDLS2 – PfMDH L-lactate dehydrogenase bound to inhibitor 6a

UniProt ID: Q6VVP7 (1-313) L-lactate dehydrogenase
L-lactate dehydrogenase experimental SAS data
DAMMIF model
Sample: L-lactate dehydrogenase tetramer, 141 kDa Plasmodium falciparum protein
Buffer: 100 mM Na-phosphate buffer, 400 mM NaCl, pH: 7.4
Experiment: SAXS data collected at Xenocs Xeuss 2.0 with MetalJet, Department of Macromolecular Physics, Faculty of Physics, Adam Mickiewicz University on 2019 Jul 3
A fragment-based approach identifies an allosteric pocket that impacts malate dehydrogenase activity Communications Biology 4(1) (2021)
Reyes Romero A, Lunev S, Popowicz G, Calderone V, Gentili M, Sattler M, Plewka J, Taube M, Kozak M, Holak T, Dömling A, Groves M
RgGuinier 3.6 nm
Dmax 11.4 nm
VolumePorod 223 nm3

SASDLT2 – 6D11 IgG monoclonal antibody

UniProt ID: None (None-None) Anti-prion protein monoclonal IgG2a 6D11
Anti-prion protein monoclonal IgG2a 6D11 experimental SAS data
CORAL model
Sample: Anti-prion protein monoclonal IgG2a 6D11 monomer, 145 kDa Mus musculus protein
Buffer: phosphate buffered saline, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Dec 15
Ligands binding to the prion protein induce its proteolytic release with therapeutic potential in neurodegenerative proteinopathies. Sci Adv 7(48):eabj1826 (2021)
Linsenmeier L, Mohammadi B, Shafiq M, Frontzek K, Bär J, Shrivastava AN, Damme M, Song F, Schwarz A, Da Vela S, Massignan T, Jung S, Correia A, Schmitz M, Puig B, Hornemann S, Zerr I, Tatzelt J, Biasini E, Saftig P, Schweizer M, Svergun D, Amin L, Mazzola F, Varani L, Thapa S, Gilch S, Schätzl H, Harris DA, Triller A, Mikhaylova M, Aguzzi A, Altmeppen HC, Glatzel M
RgGuinier 5.1 nm
Dmax 17.4 nm
VolumePorod 330 nm3

SASDLU2 – 2:1 complex between anti prion protein monoclonal IgG 6D11 and recombinant murine prion protein

UniProt ID: P04925 (23-230) Major prion protein

UniProt ID: None (None-None) Anti-prion protein monoclonal IgG2a 6D11
Major prion proteinAnti-prion protein monoclonal IgG2a 6D11 experimental SAS data
OTHER model
Sample: Major prion protein monomer, 23 kDa Mus musculus protein
Anti-prion protein monoclonal IgG2a 6D11 monomer, 145 kDa Mus musculus protein
Buffer: phosphate buffered saline, pH: 7.4
Experiment: SAXS data collected at EMBL P12, PETRA III on 2019 Dec 15
Ligands binding to the prion protein induce its proteolytic release with therapeutic potential in neurodegenerative proteinopathies. Sci Adv 7(48):eabj1826 (2021)
Linsenmeier L, Mohammadi B, Shafiq M, Frontzek K, Bär J, Shrivastava AN, Damme M, Song F, Schwarz A, Da Vela S, Massignan T, Jung S, Correia A, Schmitz M, Puig B, Hornemann S, Zerr I, Tatzelt J, Biasini E, Saftig P, Schweizer M, Svergun D, Amin L, Mazzola F, Varani L, Thapa S, Gilch S, Schätzl H, Harris DA, Triller A, Mikhaylova M, Aguzzi A, Altmeppen HC, Glatzel M
RgGuinier 8.1 nm
Dmax 24.8 nm
VolumePorod 710 nm3