MolNFT v1 · #176731 · protein

SARS-cov-2 mpro mutant (H41A) in complex with NSP5|6 peptidyl substrate

7DVW · 3C-like proteinase: “SARS-cov-2 mpro mutant (H41A) in complex with NSP5|6 peptidyl substrate”. X-ray diffraction, 2 pockets (best druggability 0.36). MolNFT v1 #176731 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DVW
Type: protein
Length: 315 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase; NSP5/6 peptidyl substrate
EC: 3.4.22.69
UniProt: P0DTD1
Pockets: 2 · best druggability 0.36

Structure

x-ray diffraction · 2 distinct chains · 24% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	306	25% helix, 29% strand	P0DTD1
C	NSP5/6 peptidyl substrate	protein	9	0% helix, 33% strand	P0DTD1

Ligands and binding sites

DMS · Dimethyl sulfoxide · additive · chains A, C

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	65	0.36	0.78	17	DMS
2	64	0.29	0.74	13	empty

Interfaces

1 interface between chains.

A–C · 658 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

7DVW · SARS-CoV-2 Mpro mutant (H41A) in complex with nsp5|6 peptidyl substrate · 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 7DVW · PDBe 7DVW · UniProt P0DTD1

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