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Structure of the human metapneumovirus fusion protein in the postfusion conformation

Analyse Structure of the human metapneumovirus fusion protein in the postfusion… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5L1X
Type: protein
Length: 2,654 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hmpv F2 subunit; Hmpv F1 subunit
UniProt: H6X1Z1, Q8B9P0
Ligands: NAG, FUC, SO4
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 6 distinct chains · 41% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, I	Hmpv F2 subunit	protein	73	30% helix, 40% strand	H6X1Z1
B, F, H	Hmpv F1 subunit	protein	369	43% helix, 30% strand	Q8B9P0
D	Hmpv F1 subunit	protein	369	43% helix, 30% strand	Q8B9P0
G, K	Hmpv F2 subunit	protein	74	27% helix, 39% strand	H6X1Z1
J	Hmpv F1 subunit	protein	368	43% helix, 30% strand	Q8B9P0
L	Hmpv F1 subunit	protein	370	42% helix, 29% strand	Q8B9P0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains B, C, E, F, H, L, G, K, D, I, J
FUC · alpha-L-fucopyranose · sugar · 5 copies · chains B, C, L, F, H
SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E, F, G, H, I, J, L

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

Pockets

20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1023	0.86	0.87	76	empty
2	1030	0.86	0.87	76	empty
3	1105	0.79	0.80	118	SO4
4	997	0.78	0.80	94	SO4
5	862	0.77	0.81	92	empty

Interfaces

35 interfaces between chains.

H–L · 4732 Å² buried · 37 hydrogen bonds · protein-protein
B–F · 4697 Å² buried · 29 hydrogen bonds · protein-protein
D–F · 4688 Å² buried · 31 hydrogen bonds · protein-protein
J–L · 4687 Å² buried · 36 hydrogen bonds · protein-protein
B–D · 4629 Å² buried · 34 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 disulfide, 12 glycan (disulfide, N-glycosylation).

Compared structures

5L1X · Structure of the Human Metapneumovirus Fusion Protein in the Postfusion Conformation · 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
Every structure of UniProt H6X1Z1
Every structure of UniProt Q8B9P0
Elsewhere: RCSB PDB 5L1X · PDBe 5L1X · UniProt H6X1Z1 · UniProt Q8B9P0

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