Research workbench

Feline calicivirus VP1 T=1 virus-like particle

Analyse Feline calicivirus VP1 T=1 virus-like particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4PB6
Type: protein
Length: 10,040 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	VP1	protein	502	5% helix, 23% strand	—

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1122	0.87	0.88	130	empty
2	1083	0.87	0.88	129	empty
3	1051	0.87	0.87	113	empty
4	955	0.86	0.88	112	empty
5	1147	0.85	0.86	154	empty

Interfaces

55 interfaces between chains.

F–N · 1479 Å² buried · 11 hydrogen bonds · protein-protein
L–S · 1479 Å² buried · 11 hydrogen bonds · protein-protein
A–E · 1477 Å² buried · 11 hydrogen bonds · protein-protein
Q–R · 1476 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 1475 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4PB6 · Feline calicivirus VP1 T=1 virus-like particle · 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 4PB6 · PDBe 4PB6

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