MolNFT v1 · #155546 · protein

Cryo-EM structure of echovirus 11 a-particle at pH 5.5

6LB1 · Capsid protein VP1: “Cryo-EM structure of echovirus 11 a-particle at pH 5.5”. Electron microscopy, 10 pockets (best druggability 0.63). MolNFT v1 #155546 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6LB1
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 0.63

Structure

electron microscopy · 3 distinct chains · 7% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	222	7% helix, 35% strand	—
B	Capsid protein VP2	protein	245	6% helix, 40% strand	—
C	Capsid protein VP3	protein	222	9% helix, 36% strand	—

Pockets

10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	183	0.63	0.84	32	empty
2	230	0.60	0.80	40	empty
3	95	0.46	0.80	21	empty
4	94	0.41	0.78	22	empty
5	108	0.41	0.76	27	empty

Interfaces

3 interfaces between chains.

A–C · 3006 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 1605 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1467 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6LB1 · Cryo-EM structure of echovirus 11 A-particle at pH 5.5 · 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 6LB1 · PDBe 6LB1

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