MolNFT v1 · #190112 · protein

Crystal structure of SARS-cov-2 3CLPRO catalytic domain

7WHC · 3C-like proteinase NSP5: “Crystal structure of SARS-cov-2 3CLPRO catalytic domain”. X-ray diffraction, 8 pockets (best druggability 0.75). MolNFT v1 #190112 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7WHC
Type: protein
Length: 728 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C-like proteinase NSP5
EC: 3.4.22.69
UniProt: P0DTD1
Pockets: 8 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 12% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	3C-like proteinase NSP5 (EC 3.4.22.69)	protein	182	12% helix, 45% strand	P0DTD1

Pockets

8 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	560	0.75	0.83	63	empty
2	142	0.59	0.84	28	empty
3	85	0.55	0.86	21	empty
4	194	0.50	0.76	35	empty
5	203	0.49	0.76	30	empty

Interfaces

5 interfaces between chains.

A–B · 425 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 311 Å² buried · 1 hydrogen bond · protein-protein
B–C · 289 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 248 Å² buried · 0 hydrogen bonds · protein-protein
C–D · 247 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

7WHC · Crystal structure of SARS-CoV-2 3CLpro catalytic domain · 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 7WHC · PDBe 7WHC · UniProt P0DTD1

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