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C6 portal vertex in the enveloped virion capsid

Analyse C6 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: 7ETM
Type: protein
Length: 5,970 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Portal protein
UniProt: Q6RXD3
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · 2 distinct chains · 55% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E, H, I, J, K, L	Portal protein	protein	497	55% helix, 9% strand	Q6RXD3
A, B, C, D, F, G	Portal protein	protein	498	55% helix, 10% strand	Q6RXD3

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	333	0.80	0.90	67	empty
2	400	0.80	0.88	58	empty
3	390	0.80	0.88	58	empty
4	327	0.80	0.90	46	empty
5	375	0.80	0.89	58	empty

Interfaces

24 interfaces between chains.

I–C · 5582 Å² buried · 55 hydrogen bonds · protein-protein
K–F · 5577 Å² buried · 51 hydrogen bonds · protein-protein
L–G · 5572 Å² buried · 55 hydrogen bonds · protein-protein
H–B · 5567 Å² buried · 51 hydrogen bonds · protein-protein
E–A · 5561 Å² buried · 53 hydrogen bonds · protein-protein

Compared structures

7ETM · C6 portal vertex in the enveloped virion capsid · the same entry in another collection · chain E against E, 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 Q6RXD3
Elsewhere: RCSB PDB 7ETM · PDBe 7ETM · UniProt Q6RXD3

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