MolNFT v1 · #189423 · protein

The complex of SARS-COV2 3CL and NB1A2

7VFA: “The complex of SARS-COV2 3CL and NB1A2”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.52). MolNFT v1 #189423 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VFA
Type: protein
Length: 419 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NB1A2; 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTC1
Ligands: SO4
Pockets: 4 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 21% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	NB1A2	protein	123	7% helix, 50% strand	—
E	3C-like proteinase (EC 3.4.22.69)	protein	296	26% helix, 29% strand	P0DTC1

Ligands and binding sites

SO4 · Sulfate ion · ion · chains E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	54	0.52	0.88	17	empty
2	188	0.49	0.76	26	empty
3	64	0.41	0.80	15	empty
4	55	0.25	0.72	13	empty

Interfaces

1 interface between chains.

D–E · 911 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7VFA · the complex of SARS-CoV2 3CL and NB1A2 · the same entry in another collection · chain D against D, 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 P0DTC1
Elsewhere: RCSB PDB 7VFA · PDBe 7VFA · UniProt P0DTC1

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