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C5 portal vertex in the enveloped virion capsid

Analyse C5 portal vertex in the enveloped virion capsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ET3
Type: protein
Length: 10,843 residues
Chains: 23
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Triplex capsid protein 2; Large tegument protein deneddylase; Triplex capsid protein 1…
EC: 3.4.19.12, 3.4.22.-
UniProt: Q6RXF2, A0A3G6XL22, Q6RXH2, A0A6C0PJD3, A0A3G6XKK5, A0A6C0PKC1, A8T7C4, A0A1U8QPG3
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 18 distinct chains · 33% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
h	Triplex capsid protein 2	protein	285	36% helix, 19% strand	Q6RXF2
I	Triplex capsid protein 2	protein	285	39% helix, 19% strand	Q6RXF2
H, P	Large tegument protein deneddylase (EC 3.4.19.12, 3.4.22.-)	protein	20	75% helix, 0% strand	A0A3G6XL22
n	Triplex capsid protein 2	protein	293	36% helix, 17% strand	Q6RXF2
o	Triplex capsid protein 2	protein	282	35% helix, 22% strand	Q6RXF2
g	Triplex capsid protein 1	protein	237	23% helix, 36% strand	Q6RXH2
m	Triplex capsid protein 1	protein	290	21% helix, 31% strand	Q6RXH2
M	Capsid vertex component 1	protein	468	28% helix, 23% strand	A0A6C0PJD3
N	Capsid vertex component 2	protein	65	54% helix, 5% strand	A0A3G6XKK5
O	Capsid vertex component 2	protein	69	55% helix, 3% strand	A0A3G6XKK5
1	ORFL92C_UL32	protein	285	61% helix, 0% strand	A0A6C0PKC1
R, S, T, i, j	Small capsomere-interacting protein	protein	63	60% helix, 0% strand	A8T7C4
a	Major capsid protein	protein	1286	31% helix, 16% strand	A0A1U8QPG3
B	Major capsid protein	protein	1332	34% helix, 14% strand	A0A1U8QPG3
C	Major capsid protein	protein	1330	35% helix, 16% strand	A0A1U8QPG3
D	Major capsid protein	protein	1297	32% helix, 15% strand	A0A1U8QPG3
Y	Major capsid protein	protein	1347	28% helix, 15% strand	A0A1U8QPG3
Z	Major capsid protein	protein	1337	33% helix, 17% strand	A0A1U8QPG3

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	932	0.88	0.90	116	empty
2	1199	0.87	0.88	131	empty
3	662	0.86	0.90	83	empty
4	702	0.84	0.88	82	empty
5	909	0.83	0.85	107	empty

Interfaces

68 interfaces between chains.

C–D · 6583 Å² buried · 67 hydrogen bonds · protein-protein
a–Z · 6544 Å² buried · 81 hydrogen bonds · protein-protein
B–C · 6543 Å² buried · 83 hydrogen bonds · protein-protein
Y–Z · 6365 Å² buried · 76 hydrogen bonds · protein-protein
n–o · 3367 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

7ET3 · C5 portal vertex in the enveloped virion capsid · the same entry in another collection · chain h against h, 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 Q6RXF2
Every structure of UniProt A0A3G6XL22
Every structure of UniProt Q6RXH2
Every structure of UniProt A0A6C0PJD3
Every structure of UniProt A0A3G6XKK5
Every structure of UniProt A0A6C0PKC1
Every structure of UniProt A8T7C4
Every structure of UniProt A0A1U8QPG3
Elsewhere: RCSB PDB 7ET3 · PDBe 7ET3 · UniProt Q6RXF2 · UniProt A0A3G6XL22 · UniProt Q6RXH2 · UniProt A0A6C0PJD3 · UniProt A0A3G6XKK5 · UniProt A0A6C0PKC1 · UniProt A8T7C4 · UniProt A0A1U8QPG3

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