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Human rhinovirus serotype 2 (HRV2)

Analyse Human rhinovirus serotype 2 (HRV2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1FPN
Type: protein
Length: 781 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coat protein VP1; Coat protein VP2; Coat protein VP3; Coat protein VP4
UniProt: P04936
Ligands: DAO
Pockets: 13 · best druggability 0.80

Structure

x-ray diffraction · 4 distinct chains · 10% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Coat protein VP1	protein	269	10% helix, 31% strand	P04936
2	Coat protein VP2	protein	250	12% helix, 37% strand	P04936
3	Coat protein VP3	protein	237	9% helix, 32% strand	P04936
4	Coat protein VP4	protein	25	12% helix, 16% strand	P04936

Ligands and binding sites

DAO · Lauric acid · ligand · chains 1

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

Pockets

13 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	208	0.80	0.93	39	DAO
2	237	0.57	0.78	25	empty
3	215	0.50	0.75	43	empty
4	128	0.49	0.79	23	empty
5	79	0.45	0.81	16	empty

Interfaces

5 interfaces between chains.

1–3 · 4135 Å² buried · 66 hydrogen bonds · protein-protein
1–2 · 2040 Å² buried · 40 hydrogen bonds · protein-protein
2–3 · 1690 Å² buried · 24 hydrogen bonds · protein-protein
3–4 · 393 Å² buried · 7 hydrogen bonds · protein-protein
1–4 · 360 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

1FPN · Human rhinovirus serotype 2 (HRV2) · 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 P04936
Elsewhere: RCSB PDB 1FPN · PDBe 1FPN · UniProt P04936

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