Research workbench
Crystal structure of the DNA-binding protein RemA from Geobacillus thermodenitrificans
Analyse Crystal structure of the DNA-binding protein RemA from Geobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BM2
- Type
- protein
- Length
- 314 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.29
- Source
- Geobacillus thermodenitrificans NG80-2
- Molecule
- Putative regulatory protein GTNG_1019
- UniProt
- A4IM41
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · resolution 2.29 · 3 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative regulatory protein GTNG_1019 | protein | 82 | 29% helix, 28% strand | A4IM41 |
| B, C | Putative regulatory protein GTNG_1019 | protein | 77 | 27% helix, 30% strand | A4IM41 |
| D | Putative regulatory protein GTNG_1019 | protein | 78 | 28% helix, 29% strand | A4IM41 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.38 | 0.79 | 13 | empty |
| 2 | 56 | 0.37 | 0.79 | 12 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1026 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1010 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1000 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 7BM2 · Crystal structure of the DNA-binding protein rema from geobacillus thermodenitrificans · the same entry in another collection · chain A against A, TM-score 1.00
- A4IM41 · AlphaFold monomer V2.0 prediction for putative regulatory protein GTNG_1019 (A4IM41) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 A4IM41
- Elsewhere: RCSB PDB 7BM2 · PDBe 7BM2 · UniProt A4IM41
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