MolNFT v1 · #118521 · protein

Protruding domain of GII.17 norovirus KAWASAKI323

5F4M · Capsid protein: “Protruding domain of GII.17 norovirus KAWASAKI323”. X-ray diffraction, 8 pockets (best druggability 0.79). MolNFT v1 #118521 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5F4M
Type: protein
Length: 613 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: A0A0A7CJV4
Pockets: 8 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	308	6% helix, 35% strand	A0A0A7CJV4
B	Capsid protein	protein	305	6% helix, 35% strand	A0A0A7CJV4

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains A, B

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

Pockets

8 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	724	0.79	0.83	115	EDO
2	129	0.68	0.89	24	empty
3	172	0.47	0.76	27	empty
4	92	0.45	0.80	19	empty
5	95	0.43	0.79	17	empty

Interfaces

1 interface between chains.

A–B · 1839 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

5F4M · Protruding domain of GII.17 norovirus Kawasaki323 · 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
Every structure of UniProt A0A0A7CJV4
Elsewhere: RCSB PDB 5F4M · PDBe 5F4M · UniProt A0A0A7CJV4

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