Research workbench
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
- 1V0U
- Type
- protein
- Length
- 490 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
- 4 · best druggability 0.75
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 | 490 | 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.75 | 0.99 | 19 | empty |
| 2 | 187 | 0.50 | 0.77 | 23 | PO3 |
| 3 | 64 | 0.35 | 0.77 | 13 | empty |
| 4 | 98 | 0.34 | 0.73 | 13 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1V0U · 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 1V0U · PDBe 1V0U
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.