MolNFT v1 · #179000 · protein
Phospholipase D engineered mutant (tnyr) H442 covalent adduct with 1- inositol phosphate
7JS7: “Phospholipase D engineered mutant (tnyr) H442 covalent adduct with 1- inositol phosphate”. X-ray diffraction, 1 ligand (IPD), 10 pockets (best druggability 0.78). MolNFT v1 #179000 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7JS7
- Type
- protein
- Length
- 985 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase D
- EC
- 3.1.4.4
- UniProt
- Q53728
- Ligands
- IPD
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase D (EC 3.1.4.4) | protein | 494 | 37% helix, 21% strand | Q53728 |
| B | Phospholipase D (EC 3.1.4.4) | protein | 491 | 35% helix, 22% strand | Q53728 |
Ligands and binding sites
- IPD · D-myo-inositol-1-phosphate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.78 | 0.80 | 86 | empty |
| 2 | 335 | 0.58 | 0.76 | 32 | IPD |
| 3 | 275 | 0.53 | 0.75 | 38 | IPD |
| 4 | 68 | 0.40 | 0.79 | 15 | MES |
| 5 | 64 | 0.38 | 0.79 | 15 | MES |
Interfaces
1 interface between chains.
- A–B · 429 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 7JS7 · Phospholipase D engineered mutant (TNYR) H442 covalent adduct with 1-inositol phosphate · 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 7JS7 · PDBe 7JS7 · UniProt Q53728
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