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Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development

Analyse Atomic structures and deletion mutant reveal different capsid-binding patterns… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NHJ
Type: protein
Length: 27,627 residues
Chains: 55
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 5.0
Source: Murine cytomegalovirus (strain Smith)
Molecule: Major capsid protein; Tegument protein; Small capsomere-interacting protein; Minor capsid…
UniProt: A0A1S5YGR4, D3XDM2, D3XDN6, D3XDN4, D3XDR2
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 5.0 · 31 distinct chains · 33% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major capsid protein	protein	1335	32% helix, 16% strand	A0A1S5YGR4
B	Major capsid protein	protein	1310	32% helix, 17% strand	A0A1S5YGR4
C	Major capsid protein	protein	1310	31% helix, 16% strand	A0A1S5YGR4
D	Major capsid protein	protein	1314	31% helix, 17% strand	A0A1S5YGR4
E	Major capsid protein	protein	1330	32% helix, 17% strand	A0A1S5YGR4
F	Major capsid protein	protein	1319	32% helix, 16% strand	A0A1S5YGR4
G, H	Major capsid protein	protein	1341	32% helix, 16% strand	A0A1S5YGR4
I	Major capsid protein	protein	1321	30% helix, 16% strand	A0A1S5YGR4
k	Major capsid protein	protein	1295	33% helix, 17% strand	A0A1S5YGR4
l	Major capsid protein	protein	1336	33% helix, 18% strand	A0A1S5YGR4
m	Major capsid protein	protein	1312	32% helix, 17% strand	A0A1S5YGR4
n	Major capsid protein	protein	1335	32% helix, 16% strand	A0A1S5YGR4
o	Major capsid protein	protein	1313	33% helix, 17% strand	A0A1S5YGR4
p	Major capsid protein	protein	1301	34% helix, 16% strand	A0A1S5YGR4
q	Major capsid protein	protein	1219	34% helix, 16% strand	A0A1S5YGR4
2, e, f, g	Tegument protein	protein	174	77% helix, 0% strand	D3XDM2
3, h, i, j	Tegument protein	protein	200	72% helix, 0% strand	D3XDM2
J, r, u, v, w	Small capsomere-interacting protein	protein	60	60% helix, 0% strand	D3XDN6
K, L, M, N, O, P, Q, R, s, t	Small capsomere-interacting protein	protein	59	64% helix, 0% strand	D3XDN6
x	Small capsomere-interacting protein	protein	57	67% helix, 0% strand	D3XDN6
y	Minor capsid protein	protein	249	25% helix, 34% strand	D3XDN4
S, T, U, V	Minor capsid protein	protein	289	27% helix, 28% strand	D3XDN4
z	Triplex capsid protein 2	protein	284	38% helix, 17% strand	D3XDR2
W, Z	Triplex capsid protein 2	protein	281	36% helix, 18% strand	D3XDR2
X	Triplex capsid protein 2	protein	277	36% helix, 20% strand	D3XDR2
Y	Triplex capsid protein 2	protein	282	37% helix, 19% strand	D3XDR2
1	Triplex capsid protein 2	protein	257	38% helix, 23% strand	D3XDR2
a	Triplex capsid protein 2	protein	267	35% helix, 23% strand	D3XDR2
b	Triplex capsid protein 2	protein	270	36% helix, 20% strand	D3XDR2
c	Triplex capsid protein 2	protein	274	35% helix, 23% strand	D3XDR2
d	Triplex capsid protein 2	protein	274	34% helix, 22% strand	D3XDR2

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	1402	0.88	0.89	110	empty
2	959	0.87	0.89	113	empty
3	1734	0.87	0.88	135	empty
4	1400	0.86	0.87	108	empty
5	1926	0.86	0.87	155	empty

Interfaces

132 interfaces between chains.

o–p · 7082 Å² buried · 111 hydrogen bonds · protein-protein
D–E · 6963 Å² buried · 105 hydrogen bonds · protein-protein
H–I · 6953 Å² buried · 111 hydrogen bonds · protein-protein
k–l · 6943 Å² buried · 100 hydrogen bonds · protein-protein
A–F · 6907 Å² buried · 107 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide (disulfide).

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 A0A1S5YGR4
Every structure of UniProt D3XDM2
Every structure of UniProt D3XDN6
Every structure of UniProt D3XDN4
Every structure of UniProt D3XDR2
Elsewhere: RCSB PDB 6NHJ · PDBe 6NHJ · UniProt A0A1S5YGR4 · UniProt D3XDM2 · UniProt D3XDN6 · UniProt D3XDN4 · UniProt D3XDR2

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