Research workbench
Tungstate-inhibited phospholipase D from streptomyces sp. strain pmf
Analyse Tungstate-inhibited phospholipase D from streptomyces sp. strain pmf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V0R
- 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
- WO5
- Pockets
- 5 · best druggability 0.74
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 | 493 | 37% helix, 23% strand | — |
Ligands and binding sites
- WO5 · Tungstate(vi) ion · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.74 | 0.99 | 18 | empty |
| 2 | 223 | 0.53 | 0.76 | 24 | WO5 |
| 3 | 107 | 0.35 | 0.73 | 14 | empty |
| 4 | 58 | 0.34 | 0.78 | 14 | empty |
| 5 | 50 | 0.25 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1V0R · Tungstate-inhibited phospholipase D from Streptomyces sp. strain PMF · 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 1V0R · PDBe 1V0R
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