MolNFT v2 · #225745 · protein

Cryo-EM structure of Dragon Grouper nervous necrosis virus-like particle at pH6.5 (2.82A)

8YF7 · Capsid protein alpha: “Cryo-EM structure of Dragon Grouper nervous necrosis virus-like particle at pH6.5 (2.82A)”. Electron microscopy at 2.82, 1 ligand (CA), 3 pockets (best druggability 0.64). MolNFT v2 #225745 on GenesisL1: 3D…

PDB: 8YF7
Type: protein
Length: 509 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.82
Source: Dragon grouper nervous necrosis virus
Molecule: Capsid protein alpha
UniProt: Q9E6H7
Ligands: CA
Pockets: 3 · best druggability 0.64

Structure

electron microscopy · resolution 2.82 · 2 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Capsid protein alpha	protein	164	12% helix, 46% strand	Q9E6H7
C	Capsid protein alpha	protein	181	10% helix, 41% strand	Q9E6H7

Ligands and binding sites

CA · Calcium ion · metal · 3 copies · chains A, C, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	298	0.64	0.81	41	empty
2	107	0.42	0.77	29	empty
3	64	0.42	0.81	21	empty

Interfaces

3 interfaces between chains.

B–C · 1131 Å² buried · 18 hydrogen bonds · protein-protein
A–B · 745 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 644 Å² buried · 12 hydrogen bonds · protein-protein

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 Q9E6H7
Elsewhere: RCSB PDB 8YF7 · PDBe 8YF7 · UniProt Q9E6H7

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