MolNFT v1 · #137128 · protein
The 2.4A crystal structure of ompa domain of ompa from salmonella enterica subsp. enterica serovar typhimurium str. 14028S
5VES · Outer membrane protein a: “The 2.4A crystal structure of ompa domain of ompa from salmonella enterica subsp. enterica serovar…”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.73). MolNFT v1 #137128 on GenesisL1…
- 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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