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The crystal structure of bacillus subtilis gabr, an autorepressor and plp- and GABA-dependent transcriptional activator of gabt
Analyse The crystal structure of bacillus subtilis gabr, an autorepressor and plp- and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MGR
- Type
- protein
- Length
- 1,878 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulatory protein gabr
- UniProt
- P94426
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulatory protein gabr | protein | 468 | 40% helix, 15% strand | P94426 |
| B | Hth-type transcriptional regulatory protein gabr | protein | 463 | 40% helix, 15% strand | P94426 |
| C | Hth-type transcriptional regulatory protein gabr | protein | 475 | 41% helix, 14% strand | P94426 |
| D | Hth-type transcriptional regulatory protein gabr | protein | 472 | 41% helix, 14% strand | P94426 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 9 copies · chains A, B, C, D
- IMD · Imidazole · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.87 | 0.92 | 85 | IMD |
| 2 | 653 | 0.84 | 0.88 | 70 | ACT |
| 3 | 262 | 0.82 | 0.93 | 41 | IMD, ACT |
| 4 | 936 | 0.79 | 0.81 | 92 | ACT, IMD |
| 5 | 393 | 0.78 | 0.88 | 50 | ACT |
Interfaces
6 interfaces between chains.
- C–D · 4519 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 4491 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 863 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 509 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 165 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4MGR · The crystal structure of Bacillus subtilis GabR, an autorepressor and PLP- and… · the same entry in another collection · chain D against D, TM-score 1.00
- P94426 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulatory protein gabr… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P94426
- Elsewhere: RCSB PDB 4MGR · PDBe 4MGR · UniProt P94426
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