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The 2.4A crystal structure of ompa domain of ompa from salmonella enterica subsp. enterica serovar typhimurium str. 14028S
Analyse The 2.4A crystal structure of ompa domain of ompa from salmonella enterica… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VES
- Type
- protein
- Length
- 255 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein a
- UniProt
- A0A0F6AZN3
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein a | protein | 127 | 38% helix, 24% strand | A0A0F6AZN3 |
| B | Outer membrane protein a | protein | 128 | 42% helix, 21% strand | A0A0F6AZN3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.73 | 0.96 | 22 | SO4 |
| 2 | 111 | 0.40 | 0.76 | 21 | SO4 |
| 3 | 90 | 0.38 | 0.77 | 20 | empty |
| 4 | 58 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 611 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, engineered).
Compared structures
- 5VES · The 2.4A crystal structure of OmpA domain of OmpA from Salmonella enterica subsp.… · 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 A0A0F6AZN3
- Elsewhere: RCSB PDB 5VES · PDBe 5VES · UniProt A0A0F6AZN3
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