MolNFT v1 · #155569 · protein

Cryo-EM structure of echovirus 11 empty particle at pH 7.4

6LBO · Capsid protein VP1: “Cryo-EM structure of echovirus 11 empty particle at pH 7.4”. Electron microscopy, 10 pockets (best druggability 0.70). MolNFT v1 #155569 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LBO
Type: protein
Length: 689 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1; Capsid protein VP2; Capsid protein VP3
Pockets: 10 · best druggability 0.70

Structure

electron microscopy · 3 distinct chains · 8% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	222	9% helix, 35% strand	—
B	Capsid protein VP2	protein	245	6% helix, 38% strand	—
C	Capsid protein VP3	protein	222	9% helix, 33% strand	—

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	301	0.70	0.84	47	empty
2	53	0.70	0.98	17	empty
3	87	0.61	0.89	23	empty
4	135	0.44	0.76	28	empty
5	117	0.41	0.75	19	empty

Interfaces

3 interfaces between chains.

A–C · 2987 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 1562 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1488 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

6LBO · Cryo-EM structure of echovirus 11 empty particle at pH 7.4 · 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 6LBO · PDBe 6LBO

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