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Crystal structure of a human metapneumovirus subtype B2 trimeric fusion protein

Analyse Crystal structure of a human metapneumovirus subtype B2 trimeric fusion protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7M0I
Type: protein
Length: 2,530 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fusion glycoprotein F2; Fusion glycoprotein F1
UniProt: C6F474
Ligands: NAG
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 40% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G, I, K, A, C, E	Fusion glycoprotein F2	protein	70	27% helix, 41% strand	C6F474
H, L	Fusion glycoprotein F1	protein	352	40% helix, 32% strand	C6F474
J	Fusion glycoprotein F1	protein	352	40% helix, 32% strand	C6F474
B, F	Fusion glycoprotein F1	protein	351	40% helix, 32% strand	C6F474
D	Fusion glycoprotein F1	protein	352	40% helix, 33% strand	C6F474

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains G, H, I, J, K, L, A, B, F, C, D, E

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

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	986	0.86	0.87	77	empty
2	1184	0.85	0.86	76	empty
3	1122	0.80	0.82	117	empty
4	1169	0.79	0.81	109	empty
5	1007	0.79	0.80	96	empty

Interfaces

23 interfaces between chains.

H–L · 4237 Å² buried · 27 hydrogen bonds · protein-protein
H–J · 4223 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 4207 Å² buried · 32 hydrogen bonds · protein-protein
J–L · 4188 Å² buried · 29 hydrogen bonds · protein-protein
D–F · 4141 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 42 disulfide, 18 glycan (disulfide, N-glycosylation).

Compared structures

7M0I · Crystal structure of a human metapneumovirus subtype B2 trimeric fusion protein · 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 C6F474
Elsewhere: RCSB PDB 7M0I · PDBe 7M0I · UniProt C6F474

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