MolNFT v1 · #119942 · protein

Cryo-EM structure of human aichi virus

5GKA · Capsid protein VP1: “Cryo-EM structure of human aichi virus”. Electron microscopy, 6 pockets (best druggability 0.72). MolNFT v1 #119942 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GKA
Type: protein
Length: 808 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein VP1; Capsid protein VP0; Genome polyprotein
Pockets: 6 · best druggability 0.72

Structure

electron microscopy · 3 distinct chains · 7% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein VP1	protein	253	8% helix, 21% strand	—
B	Capsid protein VP0	protein	333	6% helix, 17% strand	—
C	Genome polyprotein	protein	222	9% helix, 32% strand	—

Pockets

6 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	858	0.72	0.77	75	empty
2	434	0.62	0.76	39	empty
3	151	0.52	0.80	23	empty
4	181	0.49	0.77	31	empty
5	67	0.43	0.81	21	empty

Interfaces

3 interfaces between chains.

A–B · 2306 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1408 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 1391 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5GKA · cryo-EM structure of human Aichi virus · 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 5GKA · PDBe 5GKA

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