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Crystal structure of coxsackievirus A24V soaked with 6'-sialyllactose (6SL)

Analyse Crystal structure of coxsackievirus A24V soaked with 6'-sialyllactose (6SL) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Q4X
Type: protein
Length: 835 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Coxsackievirus capsid protein VP1; Coxsackievirus capsid protein VP2; Coxsackievirus…
UniProt: V9VEF3
Ligands: SIA, CA, NA, CL
Pockets: 12 · best druggability 0.79

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Coxsackievirus capsid protein VP1	protein	281	12% helix, 31% strand	V9VEF3
2	Coxsackievirus capsid protein VP2	protein	264	15% helix, 36% strand	V9VEF3
3	Coxsackievirus capsid protein VP3	protein	234	8% helix, 30% strand	V9VEF3
4	Coxsackievirus capsid protein VP4	protein	56	13% helix, 16% strand	V9VEF3

Ligands and binding sites

SIA · N-acetyl-alpha-neuraminic acid · sugar · chains 1
CA · Calcium ion · metal · 5 copies · chains 1, 4, 2, 3
NA · Sodium ion · metal · chains 1
CL · Chloride ion · ion · 5 copies · chains 1, 3, 2
HEZ · Hexane-1,6-diol · additive · 2 copies · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	588	0.79	0.84	93	empty
2	78	0.54	0.86	19	empty
3	118	0.48	0.79	29	empty
4	66	0.47	0.83	19	empty
5	184	0.46	0.75	32	empty

Interfaces

6 interfaces between chains.

1–3 · 3952 Å² buried · 75 hydrogen bonds · protein-protein
1–2 · 2437 Å² buried · 44 hydrogen bonds · protein-protein
2–3 · 1717 Å² buried · 20 hydrogen bonds · protein-protein
1–4 · 1029 Å² buried · 12 hydrogen bonds · protein-protein
3–4 · 907 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

4Q4X · Crystal structure of Coxsackievirus A24v soaked with 6'-Sialyllactose (6SL) · 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 V9VEF3
Elsewhere: RCSB PDB 4Q4X · PDBe 4Q4X · UniProt V9VEF3

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