Research workbench
Crystal structure of salmonella typhi outer membrane phospholipase (ompla) dimer with bound calcium
Analyse Crystal structure of salmonella typhi outer membrane phospholipase (ompla)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EZZ
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipase A1
- EC
- 3.1.1.32, 3.1.1.4
- UniProt
- P0A232
- Ligands
- D12, CA
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipase A1 (EC 3.1.1.32, 3.1.1.4) | protein | 255 | 8% helix, 57% strand | P0A232 |
| B | Phospholipase A1 (EC 3.1.1.32, 3.1.1.4) | protein | 256 | 7% helix, 57% strand | P0A232 |
Ligands and binding sites
- D12 · Dodecane · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 4 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.81 | 0.96 | 36 | empty |
| 2 | 144 | 0.79 | 0.96 | 36 | empty |
| 3 | 281 | 0.68 | 0.83 | 31 | D12 |
| 4 | 304 | 0.66 | 0.81 | 32 | D12 |
| 5 | 129 | 0.63 | 0.87 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1732 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7EZZ · Crystal structure of Salmonella typhi outer membrane phospholipase (OMPLA) dimer with… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A232 · AlphaFold monomer V2.0 prediction for phospholipase A1 (P0A232) · a predicted model of the same protein · chain B 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 P0A232
- Elsewhere: RCSB PDB 7EZZ · PDBe 7EZZ · UniProt P0A232
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