Research workbench

Phospholipase D from streptomyces sp. strain pmf soaked with the substrate dibutyrylphosphatidylcholine.

Analyse Phospholipase D from streptomyces sp. strain pmf soaked with the substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1V0Y
Type: protein
Length: 493 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospholipase D
EC: 3.1.4.4
Ligands: HI5
Pockets: 5 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phospholipase D (EC 3.1.4.4)	protein	493	35% helix, 23% strand	—

Ligands and binding sites

HI5 · 2-(butyryloxy)-1-{[(tetrahydroxyphosphoranyl)oxy]methyl}ethyl butyrate · ligand · chains A

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

Pockets

5 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	61	0.75	0.99	17	empty
2	203	0.51	0.76	25	HI5
3	125	0.37	0.73	16	empty
4	56	0.33	0.78	15	empty
5	81	0.31	0.73	20	empty

Modifications

Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

1V0Y · Phospholipase D from Streptomyces sp. strain PMF soaked with the substrate… · 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
Elsewhere: RCSB PDB 1V0Y · PDBe 1V0Y

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.