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Crystal structure of SARS-CoV-2 NSP3 Macrodomain in complex with ASAP-0011177-001

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

PDB: 7H09
Type: protein
Length: 336 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.39
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: Papain-like protease nsp3
EC: 3.4.19.12, 3.4.22.-
UniProt: P0DTD1
Ligands: A1AL6
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · resolution 1.39 · 1 distinct chain · 41% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Papain-like protease nsp3 (EC 3.4.19.12, 3.4.22.-)	protein	168	41% helix, 19% strand	P0DTD1

Ligands and binding sites

A1AL6 · (4M)-1-methyl-4-(4-{[(1R)-2-methyl-1-(3-oxo-3,4-dihydro-2H-pyrido[3,2-b][1,4]oxazin-6-yl)propyl]amino}-7H-pyrrolo[2,3-d]pyrimidin-6-yl)-1H-pyrazole-5-carbonitrile · ligand · 2 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	196	0.55	0.79	30	A1AL6
2	190	0.55	0.79	31	A1AL6
3	161	0.42	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 397 Å² buried · 5 hydrogen bonds · protein-protein

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Every structure of UniProt P0DTD1
Elsewhere: RCSB PDB 7H09 · PDBe 7H09 · UniProt P0DTD1

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