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The crystal structure of papain-like protease of SARS cov-2, C111S mutant, in complex with human ISG15

Analyse The crystal structure of papain-like protease of SARS cov-2, C111S mutant, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7RBS
Type: protein
Length: 2,349 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Papain-like protease; Ubiquitin-like protein ISG15
EC: 3.4.19.12
UniProt: P0DTC1, P05161
Ligands: ZN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 3 distinct chains · 25% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Papain-like protease (EC 3.4.19.12)	protein	312	27% helix, 36% strand	P0DTC1
B, D, F, H, J	Ubiquitin-like protein ISG15	protein	157	22% helix, 36% strand	P05161
C, E, G, I	Papain-like protease (EC 3.4.19.12)	protein	313	26% helix, 36% strand	P0DTC1

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains A, C, E, G, I

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	968	0.86	0.87	130	empty
2	1091	0.81	0.82	78	empty
3	1144	0.81	0.82	79	empty
4	1163	0.80	0.82	85	empty
5	1034	0.76	0.78	93	empty

Interfaces

20 interfaces between chains.

E–F · 1444 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 1440 Å² buried · 22 hydrogen bonds · protein-protein
I–J · 1408 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1404 Å² buried · 29 hydrogen bonds · protein-protein
A–B · 1368 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

7RBS · The crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex… · the same entry in another collection · chain J against J, TM-score 1.00
P05161 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein ISG15 (P05161) · a predicted model of the same protein · chain B against A, TM-score 0.83

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
Every structure of UniProt P05161
Elsewhere: RCSB PDB 7RBS · PDBe 7RBS · UniProt P0DTC1 · UniProt P05161

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