Research workbench
The asymmetric tetrameric structure of the formaldehyde sensing transcriptional repressor frmr from escherichia COLI
Analyse The asymmetric tetrameric structure of the formaldehyde sensing transcriptional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LBM
- Type
- protein
- Length
- 346 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional repressor frmr
- UniProt
- Q8X5J3
- Ligands
- FOR
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transcriptional repressor frmr | protein | 83 | 84% helix, 0% strand | Q8X5J3 |
| C, D | Transcriptional repressor frmr | protein | 90 | 84% helix, 0% strand | Q8X5J3 |
Ligands and binding sites
- FOR · Formyl group · ion · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.56 | 0.80 | 30 | empty |
| 2 | 63 | 0.32 | 0.76 | 13 | empty |
| 3 | 51 | 0.29 | 0.75 | 11 | empty |
| 4 | 50 | 0.29 | 0.76 | 12 | empty |
| 5 | 56 | 0.28 | 0.74 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–D · 1363 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1362 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 924 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 919 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 548 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 5LBM · The asymmetric tetrameric structure of the formaldehyde sensing transcriptional repressor… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8X5J3 · AlphaFold monomer V2.0 prediction for transcriptional repressor frmr (Q8X5J3) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 Q8X5J3
- Elsewhere: RCSB PDB 5LBM · PDBe 5LBM · UniProt Q8X5J3
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