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Human enterovirus 71 3C protease mutant E71D in complex with rupintrivir

Analyse Human enterovirus 71 3C protease mutant E71D in complex with rupintrivir in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3QZQ
Type: protein
Length: 705 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3C protein
UniProt: E7E815
Ligands: AG7
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3C protein	protein	176	11% helix, 53% strand	E7E815
B	3C protein	protein	176	10% helix, 53% strand	E7E815
C	3C protein	protein	178	12% helix, 52% strand	E7E815
D	3C protein	protein	175	10% helix, 53% strand	E7E815

Ligands and binding sites

AG7 · 4-{2-(4-fluoro-benzyl)-6-methyl-5-[(5-methyl-isoxazole-3-carbonyl)-amino]-4-oxo-heptanoylamino}-5-(2-oxo-pyrrolidin-3-yl)-pentanoic acid ethyl ester · ligand · 4 copies · chains A, B, C, D

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

Pockets

3 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	1006	0.77	0.79	109	empty
2	241	0.57	0.79	23	empty
3	182	0.55	0.80	25	empty

Interfaces

6 interfaces between chains.

A–D · 553 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 547 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 244 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 241 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 75 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

3QZQ · Human enterovirus 71 3C protease mutant E71D in complex with rupintrivir · 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 E7E815
Elsewhere: RCSB PDB 3QZQ · PDBe 3QZQ · UniProt E7E815

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