Research workbench
Outer membrane phospholipase a from escherichia COLI
Analyse Outer membrane phospholipase a from escherichia COLI in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QD6
- Type
- protein
- Length
- 505 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane phospholipase (ompla); Protein (outer membrane phospholipase (ompla))
- EC
- 3.1.1.32
- UniProt
- P0A921
- Ligands
- HDS, CA
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 60% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Outer membrane phospholipase (ompla) | protein | 13 | 46% helix, 0% strand | P0A921 |
| C | Protein (outer membrane phospholipase (ompla)) (EC 3.1.1.32) | protein | 240 | 7% helix, 61% strand | P0A921 |
| D | Protein (outer membrane phospholipase (ompla)) (EC 3.1.1.32) | protein | 239 | 7% helix, 61% strand | P0A921 |
Ligands and binding sites
- HDS · 1-hexadecanosulfonic acid · ligand · 2 copies · chains C, D
- CA · Calcium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.76 | 0.86 | 67 | empty |
| 2 | 352 | 0.73 | 0.85 | 60 | empty |
| 3 | 200 | 0.70 | 0.88 | 32 | empty |
| 4 | 343 | 0.66 | 0.80 | 40 | CA, HDS |
| 5 | 331 | 0.66 | 0.80 | 38 | CA, HDS |
Interfaces
5 interfaces between chains.
- C–D · 1499 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 780 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 735 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 116 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 78 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 P0A921
- Elsewhere: RCSB PDB 1QD6 · PDBe 1QD6 · UniProt P0A921
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