MolNFT v1 · #17863 · protein
Structure of the D55N mutant of phospholipase C from bacillus cereus in complex with (3S)-3,4,DI-N-hexanoyloxybutyl-1-phosphocholine
1P6D: “Structure of the D55N mutant of phospholipase C from bacillus cereus in complex with…”. X-ray diffraction, 2 ligands (3PC, ZN), 1 pocket (best druggability 0.48). MolNFT v1 #17863 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1P6D
- Type
- protein
- Length
- 245 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase C
- EC
- 3.1.4.3
- UniProt
- P09598
- Ligands
- 3PC, ZN
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase C (EC 3.1.4.3) | protein | 245 | 64% helix, 1% strand | P09598 |
Ligands and binding sites
- 3PC · (3S)-3,4-di-N-hexanoyloxybutyl-1-phosphocholine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.48 | 0.79 | 23 | ZN, 3PC |
Compared structures
- 1P6D · Structure of the D55N mutant of phospholipase C from bacillus cereus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P09598 · AlphaFold monomer V2.0 prediction for phospholipase C (P09598) · a predicted model of the same protein · 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 P09598
- Elsewhere: RCSB PDB 1P6D · PDBe 1P6D · UniProt P09598
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