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Human rhinovirus 16 coat protein in complex with antiviral compound VP65099

Analyse Human rhinovirus 16 coat protein in complex with antiviral compound VP65099 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QJY
Type: protein
Length: 804 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein VP1; Protein VP2; Protein VP3; Protein VP4
UniProt: Q82122
Ligands: W03, MYR, ZN
Pockets: 12 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Protein VP1	protein	285	15% helix, 31% strand	Q82122
2	Protein VP2	protein	252	12% helix, 37% strand	Q82122
3	Protein VP3	protein	238	9% helix, 31% strand	Q82122
4	Protein VP4	protein	29	10% helix, 28% strand	Q82122

Ligands and binding sites

W03 · 2,6-dimethyl-1-(3-[3-methyl-5-isoxazolyl]-propanyl)-4-[2-methyl-4-isoxazolyl]-phenol · ligand · chains 1, 3
MYR · Myristic acid · ligand · chains 4
ZN · Zinc ion · metal · chains 1

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

Pockets

12 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	420	0.76	0.85	68	W03
2	228	0.55	0.78	26	empty
3	319	0.55	0.76	41	empty
4	163	0.47	0.76	31	empty
5	92	0.47	0.81	19	empty

Interfaces

5 interfaces between chains.

1–3 · 4259 Å² buried · 65 hydrogen bonds · protein-protein
1–2 · 2097 Å² buried · 42 hydrogen bonds · protein-protein
2–3 · 1683 Å² buried · 16 hydrogen bonds · protein-protein
1–4 · 658 Å² buried · 6 hydrogen bonds · protein-protein
3–4 · 373 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 lipid (myristoylation).

Compared structures

1QJY · Human rhinovirus 16 coat protein in complex with antiviral compound VP65099 · the same entry in another collection · chain 1 against 1, 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 Q82122
Elsewhere: RCSB PDB 1QJY · PDBe 1QJY · UniProt Q82122

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