MolNFT v1 · #142160 · protein

P domain of GII.17-2014/15 complexed with B-trisaccharide

5ZV7 · VP1: “P domain of GII.17-2014/15 complexed with B-trisaccharide”. X-ray diffraction, 2 ligands (GLA, FUC), 6 pockets (best druggability 0.80). MolNFT v1 #142160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZV7
Type: protein
Length: 611 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: VP1
UniProt: A0A1C9I7R1
Ligands: GLA, FUC
Pockets: 6 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 5% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	VP1	protein	305	5% helix, 34% strand	A0A1C9I7R1
B	VP1	protein	306	5% helix, 34% strand	A0A1C9I7R1

Ligands and binding sites

GLA · alpha-D-galactopyranose · sugar · 4 copies · chains B, A
FUC · alpha-L-fucopyranose · sugar · 2 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	787	0.80	0.83	112	empty
2	150	0.67	0.88	23	empty
3	154	0.45	0.76	23	empty
4	97	0.45	0.79	18	empty
5	80	0.39	0.78	19	empty

Interfaces

1 interface between chains.

A–B · 1819 Å² buried · 21 hydrogen bonds · protein-protein

Compared structures

5ZV7 · P domain of GII.17-2014/15 complexed with B-trisaccharide · 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 A0A1C9I7R1
Elsewhere: RCSB PDB 5ZV7 · PDBe 5ZV7 · UniProt A0A1C9I7R1

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