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Foot-and-mouth disease virus serotype A1061 complexed with oligosaccharide receptor.

Analyse Foot-and-mouth disease virus serotype A1061 complexed with oligosaccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1ZBA
Type: protein
Length: 668 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: Q84769
Ligands: SGN, IDS
Pockets: 7 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Coat protein VP1	protein	191	16% helix, 29% strand	Q84769
2	Coat protein VP2	protein	207	10% helix, 46% strand	Q84769
3	Coat protein VP3	protein	221	9% helix, 33% strand	Q84769
4	Coat protein VP4	protein	49	22% helix, 2% strand	Q84769

Ligands and binding sites

SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains 1, 2
IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · chains 1, 2

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	665	0.79	0.84	67	empty
2	887	0.73	0.77	62	empty
3	503	0.66	0.77	44	empty
4	211	0.51	0.76	26	empty
5	164	0.49	0.77	20	empty

Interfaces

6 interfaces between chains.

1–2 · 1421 Å² buried · 21 hydrogen bonds · protein-protein
1–3 · 1156 Å² buried · 19 hydrogen bonds · protein-protein
2–3 · 864 Å² buried · 9 hydrogen bonds · protein-protein
1–4 · 773 Å² buried · 13 hydrogen bonds · protein-protein
2–4 · 234 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

1ZBA · Foot-and-Mouth Disease virus serotype A1061 complexed with oligosaccharide receptor. · 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 Q84769
Elsewhere: RCSB PDB 1ZBA · PDBe 1ZBA · UniProt Q84769

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