MolNFT v1 · #91747 · protein

Merkel cell polyomavirus VP1 in complex with disialyllactose

4FMH: “Merkel cell polyomavirus VP1 in complex with disialyllactose”. X-ray diffraction, 3 ligands (GAL, SIA, CL), 20 pockets (best druggability 0.68). MolNFT v1 #91747 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FMH
Type: protein
Length: 5,491 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1
UniProt: C0JPK1
Ligands: GAL, SIA, CL
Pockets: 20 · best druggability 0.68

Structure

x-ray diffraction · 14 distinct chains · 9% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	274	8% helix, 39% strand	C0JPK1
B, C, H	VP1	protein	280	9% helix, 38% strand	C0JPK1
D	VP1	protein	272	8% helix, 40% strand	C0JPK1
E	VP1	protein	276	8% helix, 40% strand	C0JPK1
F	VP1	protein	272	8% helix, 39% strand	C0JPK1
G, Q	VP1	protein	271	8% helix, 39% strand	C0JPK1
I, S	VP1	protein	271	9% helix, 39% strand	C0JPK1
J	VP1	protein	272	8% helix, 39% strand	C0JPK1
K	VP1	protein	274	9% helix, 39% strand	C0JPK1
L	VP1	protein	272	10% helix, 39% strand	C0JPK1
M, N, R	VP1	protein	278	9% helix, 40% strand	C0JPK1
O	VP1	protein	273	8% helix, 40% strand	C0JPK1
P	VP1	protein	275	8% helix, 39% strand	C0JPK1
T	VP1	protein	273	9% helix, 39% strand	C0JPK1

Ligands and binding sites

GAL · beta-D-galactopyranose · sugar · 7 copies · chains B, H, K, O, Q, T
SIA · N-acetyl-alpha-neuraminic acid · sugar · 7 copies · chains B, H, K, M, O, Q, T
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 · 56 copies · chains A, B, C, D, E, F, G, H, I, J, K, O, L, M, N, 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	515	0.68	0.79	46	empty
2	267	0.54	0.77	41	empty
3	231	0.54	0.78	36	GOL
4	211	0.54	0.78	37	empty
5	225	0.54	0.78	40	empty

Interfaces

42 interfaces between chains.

L–M · 2386 Å² buried · 35 hydrogen bonds · protein-protein
F–G · 2383 Å² buried · 35 hydrogen bonds · protein-protein
C–D · 2382 Å² buried · 37 hydrogen bonds · protein-protein
A–E · 2365 Å² buried · 35 hydrogen bonds · protein-protein
G–H · 2364 Å² buried · 36 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

4FMH · Merkel Cell Polyomavirus VP1 in complex with Disialyllactose · the same entry in another collection · chain J against J, 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 4FMH · PDBe 4FMH · UniProt C0JPK1

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