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SARS-cov-2 macrodomain in complex with ADP-ribose

Analyse SARS-cov-2 macrodomain in complex with ADP-ribose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Z5T
Type: protein
Length: 348 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Replicase polyprotein 1AB
EC: 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-
UniProt: P0DTD1
Ligands: APR, NA
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Replicase polyprotein 1AB (EC 3.4.19.12, 3.4.22.-, 3.4.22.69, 2.7.7.48, 3.6.4.12, 3.6.4.13, 3.1.13.-, 3.1.-.-, 2.1.1.-)	protein	174	40% helix, 18% strand	P0DTD1

Ligands and binding sites

APR · Adenosine-5-diphosphoribose · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	494	0.69	0.79	51	APR
2	219	0.61	0.81	32	APR
3	52	0.27	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 356 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6Z5T · SARS-CoV-2 Macrodomain in complex with ADP-ribose · 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 6Z5T · PDBe 6Z5T · UniProt P0DTD1

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