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Crystal structure of SARS-cov-2 NSP3 macrodomain at pH 8 (P43 crystal form)

Analyse Crystal structure of SARS-cov-2 NSP3 macrodomain at pH 8 (P43 crystal form) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TWR
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
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 40% 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	41% helix, 19% strand	P0DTD1

Ligands and binding sites

ACT · Acetate ion · additive · 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	401	0.63	0.78	34	empty
2	175	0.55	0.79	32	empty
3	133	0.53	0.80	25	ACT

Interfaces

1 interface between chains.

A–B · 512 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

7TWR · Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 8 (P43 crystal form) · 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 7TWR · PDBe 7TWR · UniProt P0DTD1

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