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Crystal structure of GII.10 P domain in complex with 300MM fucose

Analyse Crystal structure of GII.10 P domain in complex with 300MM fucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4Z4R
Type: protein
Length: 629 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 0.80

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Capsid protein	protein	314	8% helix, 36% strand	Q5F4T5
B	Capsid protein	protein	315	7% helix, 35% strand	Q5F4T5

Ligands and binding sites

FUL · beta-L-fucopyranose · sugar · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · 5 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1010	0.80	0.82	117	EDO
2	138	0.61	0.85	24	empty
3	169	0.53	0.79	25	EDO
4	84	0.34	0.74	25	empty
5	63	0.34	0.77	21	empty

Interfaces

1 interface between chains.

A–B · 1952 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

4Z4R · Crystal structure of GII.10 P domain in complex with 300mM 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 4Z4R · PDBe 4Z4R · UniProt Q5F4T5

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