MolNFT v1 · #132920 · protein

Pandda analysis group deposition -- crystal structure of SARS-cov-2 main protease in complex with pcm-0102287

5REX · 3C-like proteinase: “Pandda analysis group deposition -- crystal structure of SARS-cov-2 main protease in complex with pcm-0102287”. X-ray diffraction, 1 ligand (T4V), 4 pockets (best druggability 0.53). MolNFT v1 #132920 on…

PDB: 5REX
Type: protein
Length: 304 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase
EC: 3.4.22.69
UniProt: P0DTD1
Ligands: T4V
Pockets: 4 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C-like proteinase (EC 3.4.22.69)	protein	304	26% helix, 29% strand	P0DTD1

Ligands and binding sites

T4V · 1-{4-[(naphthalen-1-yl)methyl]piperazin-1-yl}ethan-1-one · ligand · chains A
DMS · Dimethyl sulfoxide · additive · 4 copies · chains A

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	234	0.53	0.77	27	T4V, DMS
2	82	0.46	0.81	18	DMS
3	58	0.32	0.76	15	empty
4	71	0.29	0.73	16	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

5REX · PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 main protease 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 5REX · PDBe 5REX · UniProt P0DTD1

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