MolNFT v1 · #109349 · protein

Crystal structure of P domain from norovirus strain farmington hills 2004 in complex with hbga type B (triglycan)

4X05 · Major capsid protein: “Crystal structure of P domain from norovirus strain farmington hills 2004 in complex with hbga type B…”. X-ray diffraction, 2 ligands (GLA, FUC), 12 pockets (best druggability 0.78). MolNFT v1 #109349 on…

PDB: 4X05
Type: protein
Length: 1,220 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Major capsid protein
UniProt: R4I4P2
Ligands: GLA, FUC
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Major capsid protein	protein	305	6% helix, 35% strand	R4I4P2
B, C	Major capsid protein	protein	304	6% helix, 36% strand	R4I4P2
D	Major capsid protein	protein	307	6% helix, 36% strand	R4I4P2

Ligands and binding sites

GLA · alpha-D-galactopyranose · sugar · 8 copies · chains B, A, D, C
FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B, C, D

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

Pockets

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1184	0.78	0.80	111	empty
2	53	0.72	0.99	21	empty
3	52	0.70	0.97	19	empty
4	434	0.66	0.79	54	empty
5	426	0.66	0.79	43	empty

Interfaces

5 interfaces between chains.

A–B · 1794 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1783 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 323 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 261 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 99 Å² buried · 0 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 R4I4P2
Elsewhere: RCSB PDB 4X05 · PDBe 4X05 · UniProt R4I4P2

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