MolNFT v1 · #172161 · protein
Phospholipase plab from legionella pneumophila
6ZTH · Plab phospholipase: “Phospholipase plab from legionella pneumophila”. X-ray diffraction, 1 ligand (NAD), 20 pockets (best druggability 0.76). MolNFT v1 #172161 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6ZTH
- Type
- protein
- Length
- 1,881 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plab phospholipase
- UniProt
- A0A378K488
- Ligands
- NAD
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Plab phospholipase | protein | 470 | 30% helix, 29% strand | A0A378K488 |
| B | Plab phospholipase | protein | 470 | 29% helix, 28% strand | A0A378K488 |
| C | Plab phospholipase | protein | 467 | 30% helix, 28% strand | A0A378K488 |
| D | Plab phospholipase | protein | 474 | 30% helix, 27% strand | A0A378K488 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.76 | 0.78 | 86 | NAD |
| 2 | 579 | 0.76 | 0.82 | 67 | NAD |
| 3 | 274 | 0.72 | 0.86 | 37 | empty |
| 4 | 148 | 0.71 | 0.90 | 28 | empty |
| 5 | 77 | 0.66 | 0.93 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3160 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 3120 Ų buried · 58 hydrogen bonds · protein-protein
- A–C · 1160 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1128 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 modified (engineered).
Compared structures
- 6ZTH · Phospholipase PlaB from Legionella pneumophila · 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 A0A378K488
- Elsewhere: RCSB PDB 6ZTH · PDBe 6ZTH · UniProt A0A378K488
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.