Research workbench

Echo 18 at PH5.5

Analyse Echo 18 at PH5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7XXG
Type: protein
Length: 799 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1; VP2; VP3; VP4
Ligands: PLM
Pockets: 13 · best druggability 0.79

Structure

electron microscopy · 4 distinct chains · 9% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	269	8% helix, 30% strand	—
B	VP2	protein	250	10% helix, 37% strand	—
C	VP3	protein	238	8% helix, 29% strand	—
D	VP4	protein	42	10% helix, 2% strand	—

Ligands and binding sites

PLM · Palmitic acid · ligand · chains A

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

Pockets

13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	585	0.79	0.84	80	PLM
2	70	0.74	0.98	26	empty
3	56	0.59	0.91	16	empty
4	102	0.55	0.85	23	empty
5	99	0.49	0.82	15	empty

Interfaces

6 interfaces between chains.

A–C · 4142 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 2018 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 1533 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1063 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 851 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

7XXG · Echo 18 at pH5.5 · 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
Elsewhere: RCSB PDB 7XXG · PDBe 7XXG

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