MolNFT v2 · #134771 · protein

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with Z3562259556 - (R) isomer

5SR9 · Non-structural protein 3: “PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with…”. X-ray diffraction at 1.05, 1 ligand (R0H), 3 pockets (best druggability 0.67). MolNFT v2 #134771 on…

PDB: 5SR9
Type: protein
Length: 336 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.05
Source: Severe acute respiratory syndrome coronavirus 2
Molecule: Non-structural protein 3
EC: 3.4.19.121, 3.4.22.-
UniProt: P0DTD1
Ligands: R0H
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · resolution 1.05 · 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

R0H · methyl (3R)-1-(7-fluoro-9H-pyrimido[4,5-b]indol-4-yl)-3-(hydroxymethyl)pyrrolidine-3-carboxylate · 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	461	0.67	0.78	37	empty
2	160	0.54	0.80	30	empty
3	136	0.52	0.80	25	R0H

Interfaces

1 interface between chains.

A–B · 528 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

5SR9 · 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

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 5SR9 · PDBe 5SR9 · UniProt P0DTD1

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