Research workbench
Crystal structure of ompf, an outer membrane protein from salmonella typhi
Analyse Crystal structure of ompf, an outer membrane protein from salmonella typhi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NSG
- Type
- protein
- Length
- 1,023 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein F
- Ligands
- TAM, SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Outer membrane protein F | protein | 341 | 2% helix, 52% strand | — |
Ligands and binding sites
- TAM · Tris(hydroxyethyl)aminomethane · ligand · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 80 copies · chains A, C, B
- GOL · Glycerol · additive · 38 copies · chains A, B, C
- LDA · Lauryl dimethylamine-N-oxide · additive · 17 copies · chains A, C, B
- FLC · Citrate anion · additive · 4 copies · chains C
- TLA · L(+)-tartaric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.79 | 0.93 | 34 | empty |
| 2 | 1054 | 0.71 | 0.75 | 85 | SO4 |
| 3 | 1019 | 0.71 | 0.75 | 73 | SO4, GOL, TAM, LDA |
| 4 | 629 | 0.68 | 0.77 | 62 | SO4 |
| 5 | 355 | 0.56 | 0.75 | 42 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1608 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1596 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1503 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3NSG · Crystal Structure of OmpF, an Outer Membrane Protein from Salmonella typhi · 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
- Elsewhere: RCSB PDB 3NSG · PDBe 3NSG
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