MolNFT v1 · #17228 · protein
Structure determination by mad: E.COLI trigger factor binding at the ribosomal exit tunnel.
1OMS: “Structure determination by mad: E.COLI trigger factor binding at the ribosomal exit tunnel.”. X-ray diffraction, 2 ligands (SO2, SO4), 2 pockets (best druggability 0.56). MolNFT v1 #17228 on GenesisL1: 3D structure, binding sites…
- PDB
- 1OMS
- Type
- protein
- Length
- 349 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trigger factor
- EC
- 5.2.1.8
- UniProt
- P0A850
- Ligands
- SO2, SO4
- Pockets
- 2 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trigger factor (EC 5.2.1.8) | protein | 115 | 43% helix, 24% strand | P0A850 |
| B | Trigger factor (EC 5.2.1.8) | protein | 116 | 42% helix, 24% strand | P0A850 |
| C | Trigger factor (EC 5.2.1.8) | protein | 118 | 42% helix, 26% strand | P0A850 |
Ligands and binding sites
- SO2 · Sulfur dioxide · ligand · chains B
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C
- PG4 · Tetraethylene glycol · additive · 5 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.56 | 0.76 | 31 | PG4 |
| 2 | 263 | 0.55 | 0.76 | 40 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1184 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 888 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1OMS · Structure determination by MAD: E.coli Trigger Factor binding at the ribosomal exit… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A850 · AlphaFold monomer V2.0 prediction for trigger factor (P0A850) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P0A850
- Elsewhere: RCSB PDB 1OMS · PDBe 1OMS · UniProt P0A850
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