MolNFT v2 · #134718 · protein

PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with FRESH00012962804 - (S) isomer

5SPS · 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 (S6N), 3 pockets (best druggability 0.66). MolNFT v2 #134718 on…

PDB: 5SPS
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: S6N
Pockets: 3 · best druggability 0.66

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

S6N · (3S)-6,6-dimethyl-1-(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)piperidine-3-carboxylic 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	450	0.66	0.79	37	empty
2	148	0.53	0.80	24	empty
3	158	0.52	0.79	28	S6N

Interfaces

1 interface between chains.

A–B · 525 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5SPS · 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 5SPS · PDBe 5SPS · UniProt P0DTD1

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