MolNFT v1 · #91749 · protein

Merkel cell polyomavirus VP1 in complex with GD1A oligosaccharide

4FMJ: “Merkel cell polyomavirus VP1 in complex with GD1A oligosaccharide”. X-ray diffraction, 3 ligands (SIA, GAL, CL), 20 pockets (best druggability 0.67). MolNFT v1 #91749 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4FMJ
Type: protein
Length: 5,454 residues
Chains: 20
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1
UniProt: C0JPK1
Ligands: SIA, GAL, CL
Pockets: 20 · best druggability 0.67

Structure

x-ray diffraction · 14 distinct chains · 8% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	269	7% helix, 40% strand	C0JPK1
B, H	VP1	protein	280	10% helix, 38% strand	C0JPK1
C	VP1	protein	276	9% helix, 39% strand	C0JPK1
D, O	VP1	protein	271	8% helix, 39% strand	C0JPK1
E, F, L	VP1	protein	272	9% helix, 39% strand	C0JPK1
G	VP1	protein	271	9% helix, 39% strand	C0JPK1
I	VP1	protein	268	9% helix, 41% strand	C0JPK1
J	VP1	protein	270	9% helix, 40% strand	C0JPK1
K	VP1	protein	273	8% helix, 40% strand	C0JPK1
M, Q, T	VP1	protein	271	8% helix, 39% strand	C0JPK1
N	VP1	protein	278	8% helix, 40% strand	C0JPK1
P	VP1	protein	271	7% helix, 39% strand	C0JPK1
R	VP1	protein	277	7% helix, 39% strand	C0JPK1
S	VP1	protein	270	9% helix, 40% strand	C0JPK1

Ligands and binding sites

SIA · N-acetyl-alpha-neuraminic acid · sugar · 7 copies · chains K, M, O, Q, S, T, H
GAL · beta-D-galactopyranose · sugar · 6 copies · chains K, M, 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 · 8 copies · chains A, C, K, M, D, N, P, Q, 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	607	0.67	0.77	64	empty
2	455	0.64	0.77	47	GOL
3	416	0.63	0.77	52	empty
4	470	0.61	0.75	73	empty
5	195	0.56	0.80	37	empty

Interfaces

29 interfaces between chains.

C–D · 2420 Å² buried · 34 hydrogen bonds · protein-protein
G–H · 2395 Å² buried · 34 hydrogen bonds · protein-protein
L–M · 2393 Å² buried · 34 hydrogen bonds · protein-protein
N–O · 2392 Å² buried · 36 hydrogen bonds · protein-protein
F–J · 2391 Å² buried · 34 hydrogen bonds · protein-protein

Compared structures

4FMJ · Merkel cell polyomavirus VP1 in complex with GD1a oligosaccharide · 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 4FMJ · PDBe 4FMJ · UniProt C0JPK1

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