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Phospholipase D from streptomyces sp. strain pmf soaked with the product glycerophosphate

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

PDB: 1V0T
Type: protein
Length: 491 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phospholipase D
EC: 3.1.4.4
Ligands: PO3
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phospholipase D (EC 3.1.4.4)	protein	491	37% helix, 23% strand	—

Ligands and binding sites

PO3 · Phosphite ion · ion · 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	54	0.73	0.99	17	empty
2	202	0.51	0.77	27	PO3
3	62	0.35	0.78	13	empty
4	104	0.35	0.73	14	empty
5	67	0.29	0.73	19	empty

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1V0T · Phospholipase D from Streptomyces sp. strain PMF soaked with the product glycerophosphate · 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 1V0T · PDBe 1V0T

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