MolNFT v1 · #133325 · protein

Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with ZINC000002977810

5RVK · Non-structural protein 3: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with…”. X-ray diffraction, 1 ligand (2AK), 1 pocket (best druggability 0.53). MolNFT v1 #133325 on GenesisL1…

PDB: 5RVK
Type: protein
Length: 168 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Non-structural protein 3
EC: 3.4.19.121, 3.4.22.-
UniProt: P0DTD1
Ligands: 2AK
Pockets: 1 · best druggability 0.53

Structure

x-ray diffraction · 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

2AK · 7-bromo-5-methyl-1H-indole-2,3-dione · 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	184	0.53	0.78	37	empty

Compared structures

5RVK · 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 5RVK · PDBe 5RVK · UniProt P0DTD1

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