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Merkel cell polyomavirus VP1 unassembled pentamer

Analyse Merkel cell polyomavirus VP1 unassembled pentamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FMG
Type: protein
Length: 5,430 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1
UniProt: C0JPK1
Ligands: CL
Pockets: 20 · best druggability 0.67

Structure

x-ray diffraction · 15 distinct chains · 9% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E, I, S	VP1	protein	271	7% helix, 39% strand	C0JPK1
B	VP1	protein	273	10% helix, 39% strand	C0JPK1
C	VP1	protein	276	8% helix, 39% strand	C0JPK1
D	VP1	protein	271	8% helix, 39% strand	C0JPK1
F	VP1	protein	272	8% helix, 39% strand	C0JPK1
G, Q	VP1	protein	271	8% helix, 39% strand	C0JPK1
H	VP1	protein	277	10% helix, 39% strand	C0JPK1
J	VP1	protein	271	8% helix, 39% strand	C0JPK1
K	VP1	protein	272	9% helix, 39% strand	C0JPK1
L	VP1	protein	270	9% helix, 40% strand	C0JPK1
M	VP1	protein	269	9% helix, 39% strand	C0JPK1
N, R	VP1	protein	270	7% helix, 39% strand	C0JPK1
O	VP1	protein	270	9% helix, 40% strand	C0JPK1
P	VP1	protein	273	8% helix, 39% strand	C0JPK1
T	VP1	protein	270	9% helix, 40% strand	C0JPK1

Ligands and binding sites

CL · Chloride ion · ion · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
GOL · Glycerol · additive · 32 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T

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	487	0.67	0.79	42	empty
2	505	0.62	0.75	58	GOL, CL
3	223	0.55	0.79	42	empty
4	207	0.54	0.79	36	empty
5	123	0.54	0.83	29	empty

Interfaces

42 interfaces between chains.

C–D · 2391 Å² buried · 35 hydrogen bonds · protein-protein
I–J · 2387 Å² buried · 34 hydrogen bonds · protein-protein
A–E · 2380 Å² buried · 32 hydrogen bonds · protein-protein
F–G · 2379 Å² buried · 35 hydrogen bonds · protein-protein
L–M · 2370 Å² buried · 36 hydrogen bonds · protein-protein

Compared structures

4FMG · Merkel Cell Polyomavirus VP1 Unassembled Pentamer · the same entry in another collection · chain S against S, 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 C0JPK1
Elsewhere: RCSB PDB 4FMG · PDBe 4FMG · UniProt C0JPK1

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