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Human rhinovirus 16 coat protein at high resolution

Analyse Human rhinovirus 16 coat protein at high resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1AYM
Type: protein
Length: 804 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human rhinovirus 16 coat protein
UniProt: Q82122, P23008
Ligands: DAO, MYR, ZN
Pockets: 16 · best druggability 0.81

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Human rhinovirus 16 coat protein	protein	285	15% helix, 32% strand	Q82122
2	Human rhinovirus 16 coat protein	protein	252	13% helix, 37% strand	Q82122
3	Human rhinovirus 16 coat protein	protein	238	8% helix, 31% strand	Q82122
4	Human rhinovirus 16 coat protein	protein	29	10% helix, 28% strand	P23008

Ligands and binding sites

DAO · Lauric acid · ligand · chains 1
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

16 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	197	0.81	0.94	35	DAO
2	217	0.55	0.78	26	empty
3	318	0.55	0.75	40	empty
4	103	0.48	0.80	22	empty
5	131	0.42	0.75	25	empty

Interfaces

5 interfaces between chains.

1–3 · 4268 Å² buried · 64 hydrogen bonds · protein-protein
1–2 · 2089 Å² buried · 42 hydrogen bonds · protein-protein
2–3 · 1684 Å² buried · 18 hydrogen bonds · protein-protein
1–4 · 644 Å² buried · 8 hydrogen bonds · protein-protein
3–4 · 377 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 lipid (myristoylation).

Compared structures

1AYM · Human rhinovirus 16 coat protein at high resolution · 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
Every structure of UniProt P23008
Elsewhere: RCSB PDB 1AYM · PDBe 1AYM · UniProt Q82122 · UniProt P23008

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