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Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with POB0012

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: 5S3Y
Type: protein
Length: 334 residues
Chains: 2
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: W2Y
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-)	protein	165	41% helix, 21% strand	P0DTD1
B	Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-)	protein	169	42% helix, 20% strand	P0DTD1

Ligands and binding sites

W2Y · (2S,3S)-2-methyl-1-(methylsulfonyl)piperidine-3-carboxamide · ligand · chains 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	453	0.67	0.79	35	empty
2	151	0.54	0.80	25	empty
3	138	0.53	0.80	23	empty

Interfaces

1 interface between chains.

A–B · 547 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

5S3Y · 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

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Every structure of UniProt P0DTD1
Elsewhere: RCSB PDB 5S3Y · PDBe 5S3Y · UniProt P0DTD1

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