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Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses

Analyse Structural analysis of antiviral agents that interact with the capsid of human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2R07
Type: protein
Length: 804 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human rhinovirus 14 coat protein (subunit VP1); Human rhinovirus 14 coat protein (subunit…
UniProt: P03303
Ligands: W33
Pockets: 11 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 12% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Human rhinovirus 14 coat protein (subunit VP1)	protein	273	10% helix, 32% strand	P03303
2	Human rhinovirus 14 coat protein (subunit VP2)	protein	255	15% helix, 37% strand	P03303
3	Human rhinovirus 14 coat protein (subunit VP3)	protein	236	9% helix, 32% strand	P03303
4	Human rhinovirus 14 coat protein (subunit VP4)	protein	40	18% helix, 3% strand	P03303

Ligands and binding sites

W33 · 5-(5-(6-chloro-4-(4,5-dihydro-2-oxazolyl)phenoxy)pentyl)-3-methyl isoxazole · ligand · chains 1, 3

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

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	287	0.81	0.92	37	W33
2	195	0.53	0.78	35	empty
3	168	0.46	0.76	34	empty
4	96	0.43	0.79	22	empty
5	110	0.40	0.76	21	empty

Interfaces

6 interfaces between chains.

1–3 · 4141 Å² buried · 67 hydrogen bonds · protein-protein
1–2 · 2109 Å² buried · 45 hydrogen bonds · protein-protein
2–3 · 1705 Å² buried · 15 hydrogen bonds · protein-protein
1–4 · 955 Å² buried · 14 hydrogen bonds · protein-protein
3–4 · 898 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

2R07 · Structural analysis of antiviral agents that interact with the capsid of human… · the same entry in another collection · chain 2 against 2, 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 P03303
Elsewhere: RCSB PDB 2R07 · PDBe 2R07 · UniProt P03303

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