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Crystal structure of SARS-cov-2 macrodomain in complex with gmp

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

PDB: 7BF4
Type: protein
Length: 170 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NSP3 macrodomain
EC: 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
UniProt: P0DTD1
Ligands: 5GP
Pockets: 1 · best druggability 0.52

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NSP3 macrodomain (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-)	protein	170	41% helix, 19% strand	P0DTD1

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · chains A
EDO · 1,2-ethanediol · additive · 9 copies · 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	197	0.52	0.77	37	EDO

Compared structures

7BF4 · Crystal structure of SARS-CoV-2 macrodomain in complex with GMP · 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 7BF4 · PDBe 7BF4 · UniProt P0DTD1

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