Lab/Institutional Collections
Datasets

X-Ray Diffraction data from nanobody complex with IL2Rb, source of 7S2S structure

native dataset

X-Ray Diffraction data from nanobody complex with IL2Rg, source of 7S2R structure

native dataset

PDHc Core Scaffold structure from C. thermophilum

Structural model of the E3BP core, refined in a C2 symmetrized cryoEM map. E3BP showed a minimal fold, which is conserved, and can be found in various other E2 proteins from diverse acyl-transferases, including the 2-keto acid dehydrogenase family. Additionally, by fitting the structural models into an asymmetrically refined cryoEM map, we supply a structural model for the native core scaffold of the PDHc metabolon from C. thermophilum. Models were built and refined by COOT and PHENIX. To capture the transient interaction of lipoyl domain (LD) and the core structure during the transacetylase reaction, we docked the LDs of C. thermophilum, H. sapiens, and N. crassa to their respective core structure. HADDOCK parameter files are deposited to reproduce docking. The best docking solution of C. thermophilum was used to study the interaction by extensive MD simulations. Parameter files and results are also given, to reproduce these simulations.

X-Ray Diffraction data from Human thrombin:tsetse thrombin inhibitor complex, source of 7PHX structure

Human thrombin:tsetse thrombin inhibitor complex, source of 7PHX structure

X-Ray Diffraction data from Protein tyrosine phosphatase 1B, source of 7RIN structure

Apo PTP1B by Native S-SAD at Room Temperature

X-Ray Diffraction data from Putative DNA repair helicase RadD, with ADP, at 2.03 Angstrom., source of 7R7J structure

Collected at APS on beamline LS-Cat D. 0-360 degrees rotation one degree frames. MARR 300 CCD.

Protein-protein structures

HADDOCK refined 3D structures from multiple datasets (BM5, MANY, DC, CAPRI), used for experiments in the DeepRank paper. 1.Renaud, N. et al. DeepRank: A deep learning framework for data mining 3D protein-protein interfaces. bioRxiv 2021.01.29.425727 (2021) doi:10.1101/2021.01.29.425727.

Microcrystal Electron Diffraction data from Tetragonal lysozyme, source of structure

MicroED data of tetragonal lysozyme collected from specimens prepared by Vitrobot and Preassis.

X-Ray Diffraction data from TrkA ECD complex with designed miniprotein ligand, source of 7N3T structure

native dataset

X-Ray Diffraction data from SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody B6, source of 7R98 structure

Native dataset

X-Ray Diffraction data from SARS-CoV-2 N protein RNA-binding domain bound to single-domain antibody C2, source of 7N0R structure

Process to 1.42 A

X-Ray Diffraction data from SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2, source of 7N0I structure

Native dataset

X-Ray Diffraction data from Protein tyrosine phosphatase 1B, source of 7MM1 structure

PTP1B in complex with TCS401 by Native S-SAD at Room Temperature

X-Ray Diffraction data from S95A ClbP bound to monoolein, source of 7MDE structure

Data collected at the selenium edge of a single crystal of selenomethionine-substituted ClbP grown in a monoolein mesophase.

X-Ray Diffraction data from Wildtype ClbP inhibited by hexanoyl-D-asparagine boronic acid, source of 7MDC structure

Data collected from a single crystal of the wildtype ClbP peptidase covalently inhibited by a boronic acid and grown in a monopalmitolein mesophase.

X-Ray Diffraction data from S95A ClbP bound to acyl-D-asparagine product analog, source of 7MDF structure

Bromine edge data collected from two crystals of the ClbP peptidase grown in presence of a substrate analog and in a monopalmitolein mesophase.

X-Ray Diffraction data from IL23/IL23R/IL12Rb1 signaling complex, source of 6WDQ structure

native

X-Ray Diffraction data from Interleukin-12 recepter subunit beta-1, source of 6WDP structure

SeMet dataset

X-Ray Diffraction data from Interleukin-12 recepter subunit beta-1, source of 6WDP structure

Native dataset

X-Ray Diffraction data from V. polyspora Hop1 PHD-WHD, source of 7M0P structure

Zinc anomalous SAD dataset for V. polyspora Hop1 PHD-WHD domain