MolNFT v1 · #6039 · protein
The first crystal structure of a phospholipase D
1F0I: “The first crystal structure of a phospholipase D”. X-ray diffraction, 1 ligand (PO4), 5 pockets (best druggability 0.75). MolNFT v1 #6039 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1F0I
- Type
- protein
- Length
- 496 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase D
- EC
- 3.1.4.4
- UniProt
- Q93HV1
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase D (EC 3.1.4.4) | protein | 496 | 36% helix, 22% strand | Q93HV1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · 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 | 65 | 0.75 | 0.99 | 19 | empty |
| 2 | 220 | 0.53 | 0.77 | 27 | PO4 |
| 3 | 152 | 0.48 | 0.77 | 25 | empty |
| 4 | 62 | 0.34 | 0.77 | 15 | empty |
| 5 | 78 | 0.30 | 0.73 | 20 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1F0I · The first crystal structure of a phospholipase D · 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
- Every structure of UniProt Q93HV1
- Elsewhere: RCSB PDB 1F0I · PDBe 1F0I · UniProt Q93HV1
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