Research workbench
Phospholipase D engineered mutant bound to phosphatidic acid (30 minute soak)
Analyse Phospholipase D engineered mutant bound to phosphatidic acid (30 minute soak) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JRV
- Type
- protein
- Length
- 501 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase D
- EC
- 3.1.4.4
- UniProt
- Q53728
- Ligands
- VHY
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase D (EC 3.1.4.4) | protein | 501 | 33% helix, 21% strand | Q53728 |
Ligands and binding sites
- VHY · (2R)-3-(phosphonooxy)propane-1,2-diyl dibutanoate · ligand · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.71 | 0.85 | 39 | VHY |
| 2 | 95 | 0.50 | 0.82 | 27 | GOL |
| 3 | 73 | 0.38 | 0.78 | 16 | MES |
| 4 | 54 | 0.37 | 0.80 | 16 | empty |
| 5 | 69 | 0.32 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7JRV · Phospholipase D engineered mutant bound to phosphatidic acid (30 minute soak) · the same entry in another collection · chain A against A, TM-score 1.00
- Q53728 · AlphaFold monomer V2.0 prediction for phospholipase D (Q53728) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 7JRV · PDBe 7JRV · UniProt Q53728
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