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Structure of seneca valley virus in acidic conditions

Analyse Structure of seneca valley virus in acidic conditions in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ADS
Type: protein
Length: 769 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP3; VP2; VP4
Pockets: 12 · best druggability 0.69

Structure

electron microscopy · 4 distinct chains · 8% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	252	8% helix, 32% strand	—
C	VP3	protein	228	9% helix, 29% strand	—
B	VP2	protein	254	7% helix, 34% strand	—
D	VP4	protein	35	11% helix, 11% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	187	0.69	0.87	27	empty
2	167	0.50	0.78	29	empty
3	119	0.46	0.78	21	empty
4	56	0.44	0.84	15	empty
5	101	0.43	0.78	19	empty

Interfaces

6 interfaces between chains.

A–C · 3339 Å² buried · 57 hydrogen bonds · protein-protein
A–B · 2689 Å² buried · 38 hydrogen bonds · protein-protein
C–B · 1667 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 913 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 557 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6ADS · Structure of Seneca Valley Virus in acidic conditions · the same entry in another collection · chain A against A, 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
Elsewhere: RCSB PDB 6ADS · PDBe 6ADS

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