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PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ZINC000020269197

Analyse PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5RVV
Type: protein
Length: 168 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.42
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: Non-structural protein 3
EC: 3.4.19.121, 3.4.22.-
UniProt: P0DTD1
Ligands: WB1
Pockets: 1 · best druggability 0.55

Structure

x-ray diffraction · resolution 1.42 · 1 distinct chain · 42% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-)	protein	168	42% helix, 19% strand	P0DTD1

Ligands and binding sites

WB1 · 6-methyl-1H-indole-3-carboxylic acid · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	214	0.55	0.78	32	empty

Compared structures

5RVV · Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0DTD1
Elsewhere: RCSB PDB 5RVV · PDBe 5RVV · UniProt P0DTD1

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