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Pandda analysis group deposition -- crystal structure of SARS-cov-2 NSP3 macrodomain in complex with ZINC000000332752

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: 5RTJ
Type: protein
Length: 336 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: PHB
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 41% 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	167	40% helix, 19% strand	P0DTD1
B	Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-)	protein	169	42% helix, 19% strand	P0DTD1

Ligands and binding sites

PHB · P-hydroxybenzoic acid · ligand · chains A

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	464	0.67	0.79	36	empty
2	132	0.52	0.80	28	PHB
3	138	0.51	0.79	25	empty

Interfaces

1 interface between chains.

A–B · 527 Å² buried · 20 hydrogen bonds · protein-protein

Analyse

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

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