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Structure of finch polyomavirus VP1 in complex with 2-O-methyl-5-N- acetyl-alpha-D-neuraminic acid

Analyse Structure of finch polyomavirus VP1 in complex with 2-O-methyl-5-N… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6Y6A
Type: protein
Length: 10,494 residues
Chains: 40
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1
UniProt: R4UMH0
Ligands: SIA, MG, CL
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 20 distinct chains · 6% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, J, K, n	Capsid protein VP1	protein	267	6% helix, 39% strand	R4UMH0
B, G, H, Z, i, j	Capsid protein VP1	protein	260	7% helix, 40% strand	R4UMH0
D, S, U, X, Y, a, e, h	Capsid protein VP1	protein	261	7% helix, 40% strand	R4UMH0
E	Capsid protein VP1	protein	263	6% helix, 40% strand	R4UMH0
F, Q	Capsid protein VP1	protein	268	6% helix, 39% strand	R4UMH0
I	Capsid protein VP1	protein	268	6% helix, 40% strand	R4UMH0
L, W	Capsid protein VP1	protein	262	6% helix, 40% strand	R4UMH0
M, g	Capsid protein VP1	protein	269	6% helix, 39% strand	R4UMH0
N	Capsid protein VP1	protein	266	6% helix, 39% strand	R4UMH0
O	Capsid protein VP1	protein	262	6% helix, 40% strand	R4UMH0
P	Capsid protein VP1	protein	269	6% helix, 39% strand	R4UMH0
R	Capsid protein VP1	protein	263	6% helix, 41% strand	R4UMH0
T	Capsid protein VP1	protein	263	6% helix, 40% strand	R4UMH0
V	Capsid protein VP1	protein	265	6% helix, 40% strand	R4UMH0
b, d	Capsid protein VP1	protein	260	7% helix, 40% strand	R4UMH0
c	Capsid protein VP1	protein	256	7% helix, 41% strand	R4UMH0
f	Capsid protein VP1	protein	261	7% helix, 40% strand	R4UMH0
k	Capsid protein VP1	protein	263	5% helix, 40% strand	R4UMH0
l	Capsid protein VP1	protein	235	3% helix, 40% strand	R4UMH0
m	Capsid protein VP1	protein	259	7% helix, 40% strand	R4UMH0

Ligands and binding sites

SIA · N-acetyl-alpha-neuraminic acid · sugar · 29 copies · chains A, E, B, C, D, F, J, G, H, I, K, O, L, M, N, P, Q, R, S, T, U, V, W, X, Y, Z, d, a, b, c, e, i, f, j, n, m
MG · Magnesium ion · metal · chains C
CL · Chloride ion · ion · 53 copies · chains B, C, D, G, J, L, M, N, O, P, Q, S, T, U, Y, Z, e, f, g, h, j, n

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

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	514	0.75	0.83	71	empty
2	903	0.69	0.75	71	CL
3	54	0.68	0.96	15	empty
4	241	0.68	0.85	42	empty
5	656	0.66	0.75	55	empty

Interfaces

109 interfaces between chains.

e–i · 2393 Å² buried · 46 hydrogen bonds · protein-protein
Z–a · 2393 Å² buried · 44 hydrogen bonds · protein-protein
S–T · 2392 Å² buried · 44 hydrogen bonds · protein-protein
B–C · 2386 Å² buried · 43 hydrogen bonds · protein-protein
Z–d · 2385 Å² buried · 43 hydrogen bonds · protein-protein

Compared structures

6Y6A · Structure of Finch Polyomavirus VP1 in complex with… · the same entry in another collection · chain i against i, 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 R4UMH0
Elsewhere: RCSB PDB 6Y6A · PDBe 6Y6A · UniProt R4UMH0

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