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Ligand-bound structure of cavally virus 3CL protease

Analyse Ligand-bound structure of cavally virus 3CL protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LAK
Type: protein
Length: 1,198 residues
Chains: 7
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3CL protease; Bez-tyr-tyr-asn-ecc peptide inhibitor
UniProt: F8RL29
Ligands: BEZ
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 26% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	3CL protease	protein	303	26% helix, 28% strand	F8RL29
B	3CL protease	protein	294	27% helix, 28% strand	F8RL29
D	3CL protease	protein	286	24% helix, 28% strand	F8RL29
I, J, K	Bez-tyr-tyr-asn-ecc peptide inhibitor	protein	4	0% helix, 50% strand	—

Ligands and binding sites

BEZ · Benzoic acid · ligand · 3 copies · chains A, I, C, J, B, K
1PE · Pentaethylene glycol · additive · 3 copies · chains A, C, D
PGE · Triethylene glycol · additive · 2 copies · chains B, C

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	239	0.84	0.96	38	empty
2	226	0.83	0.96	36	empty
3	389	0.56	0.74	40	empty
4	120	0.53	0.81	23	empty
5	140	0.50	0.79	27	empty

Interfaces

9 interfaces between chains.

A–B · 1819 Å² buried · 34 hydrogen bonds · protein-protein
C–D · 1662 Å² buried · 30 hydrogen bonds · protein-protein
C–J · 543 Å² buried · 14 hydrogen bonds · protein-protein
A–I · 543 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 536 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent, 3 modified (covalent ligand, nonstandard).

Compared structures

5LAK · Ligand-bound structure of Cavally Virus 3CL Protease · the same entry in another collection · chain B against B, 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 F8RL29
Elsewhere: RCSB PDB 5LAK · PDBe 5LAK · UniProt F8RL29

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