MolNFT v1 · #111916 · protein

Crystal structure of GII.10 P domain in complex with 4.7MM fucose

4Z4W · Capsid protein: “Crystal structure of GII.10 P domain in complex with 4.7MM fucose”. X-ray diffraction, 1 ligand (FUL), 6 pockets (best druggability 0.75). MolNFT v1 #111916 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4Z4W
Type: protein
Length: 622 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Capsid protein
UniProt: Q5F4T5
Ligands: FUL
Pockets: 6 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	314	8% helix, 39% strand	Q5F4T5
B	Capsid protein	protein	308	7% helix, 37% strand	Q5F4T5

Ligands and binding sites

FUL · beta-L-fucopyranose · sugar · chains A, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	603	0.75	0.82	80	empty
2	457	0.69	0.80	52	empty
3	139	0.63	0.86	24	empty
4	155	0.51	0.79	24	EDO
5	80	0.33	0.75	17	EDO

Interfaces

1 interface between chains.

A–B · 1877 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

4Z4W · Crystal structure of GII.10 P domain in complex with 4.7mM fucose · 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 Q5F4T5
Elsewhere: RCSB PDB 4Z4W · PDBe 4Z4W · UniProt Q5F4T5

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