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Crystal structure of phospholipase D from streptomyces antibioticus
Analyse Crystal structure of phospholipase D from streptomyces antibioticus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZE4
- Type
- protein
- Length
- 501 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- Streptomyces antibioticus
- Molecule
- Phospholipase D
- EC
- 3.1.4.4
- UniProt
- Q53728
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.5 · 1 distinct chain · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase D (EC 3.1.4.4) | protein | 501 | 35% helix, 22% strand | Q53728 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.76 | 0.98 | 17 | empty |
| 2 | 287 | 0.67 | 0.82 | 38 | empty |
| 3 | 120 | 0.41 | 0.76 | 28 | empty |
| 4 | 76 | 0.41 | 0.79 | 17 | MES |
| 5 | 67 | 0.39 | 0.79 | 17 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 Q53728
- Elsewhere: RCSB PDB 2ZE4 · PDBe 2ZE4 · UniProt Q53728
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