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Crystal structure of ADP ribose phosphatase of NSP3 from SARS cov-2 in the complex with ADP ribose

Analyse Crystal structure of ADP ribose phosphatase of NSP3 from SARS cov-2 in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6W02
Type: protein
Length: 332 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: APR
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 39% 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	165	39% helix, 19% strand	P0DTD1
B	Non-structural protein 3 (EC 3.4.19.121, 3.4.22.-)	protein	167	38% helix, 19% strand	P0DTD1

Ligands and binding sites

APR · Adenosine-5-diphosphoribose · ligand · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

2 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	239	0.63	0.81	33	APR
2	197	0.59	0.81	31	APR

Interfaces

1 interface between chains.

A–B · 316 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6W02 · Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in the complex with… · 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 6W02 · PDBe 6W02 · UniProt P0DTD1

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