MolNFT v1 · #24609 · protein

Endosialidase of bacteriophage K1F

1V0E · Endo-alpha-sialidase: “Endosialidase of bacteriophage K1F”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.87). MolNFT v1 #24609 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1V0E
Type: protein
Length: 3,996 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endo-alpha-sialidase
EC: 3.2.1.129
UniProt: Q858B1
Ligands: PO4
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 3% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Endo-alpha-sialidase (EC 3.2.1.129)	protein	666	3% helix, 43% strand	Q858B1

Ligands and binding sites

PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1168	0.87	0.88	188	empty
2	523	0.86	0.92	104	empty
3	857	0.84	0.86	105	empty
4	73	0.77	0.98	18	empty
5	70	0.77	0.98	18	empty

Interfaces

11 interfaces between chains.

E–F · 7481 Å² buried · 151 hydrogen bonds · protein-protein
A–C · 7435 Å² buried · 151 hydrogen bonds · protein-protein
B–C · 7429 Å² buried · 149 hydrogen bonds · protein-protein
A–B · 7427 Å² buried · 149 hydrogen bonds · protein-protein
D–F · 7426 Å² buried · 146 hydrogen bonds · protein-protein

Compared structures

1V0E · Endosialidase of Bacteriophage K1F · 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 Q858B1
Elsewhere: RCSB PDB 1V0E · PDBe 1V0E · UniProt Q858B1

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