MolNFT v1 · #56407 · protein
Crystal structure of H168A mutant of phospholipase D from streptomyces antibioticus, as a complex with phosphatidylcholine
2ZE9: “Crystal structure of H168A mutant of phospholipase D from streptomyces antibioticus, as a complex with…”. X-ray diffraction, 1 ligand (PD7), 6 pockets (best druggability 0.76). MolNFT v1 #56407 on GenesisL1: 3D structure, binding…
- PDB
- 2ZE9
- Type
- protein
- Length
- 504 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
- PD7
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase D (EC 3.1.4.4) | protein | 504 | 35% helix, 20% strand | Q53728 |
Ligands and binding sites
- PD7 · (2R)-3-(phosphonooxy)propane-1,2-diyl diheptanoate · ligand · chains A
- 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.76 | 0.99 | 18 | empty |
| 2 | 514 | 0.75 | 0.83 | 51 | PD7 |
| 3 | 64 | 0.36 | 0.78 | 16 | empty |
| 4 | 59 | 0.35 | 0.78 | 22 | empty |
| 5 | 61 | 0.30 | 0.75 | 12 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2ZE9 · Crystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a… · 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 2ZE9 · PDBe 2ZE9 · UniProt Q53728
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