Research workbench
Crystal structure of bacillus subtilis gabr, an autorepressor and transcriptional activator of gabt
Analyse Crystal structure of bacillus subtilis gabr, an autorepressor and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4N0B
- Type
- protein
- Length
- 1,863 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
- ACE, ZN, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulatory protein gabr | protein | 469 | 38% helix, 14% strand | P94426 |
| B | Hth-type transcriptional regulatory protein gabr | protein | 465 | 42% helix, 14% strand | P94426 |
| C | Hth-type transcriptional regulatory protein gabr | protein | 463 | 40% helix, 14% strand | P94426 |
| D | Hth-type transcriptional regulatory protein gabr | protein | 466 | 38% helix, 13% strand | P94426 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains 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 | 321 | 0.85 | 0.95 | 48 | empty |
| 2 | 569 | 0.81 | 0.87 | 69 | empty |
| 3 | 390 | 0.80 | 0.89 | 64 | empty |
| 4 | 105 | 0.72 | 0.93 | 32 | empty |
| 5 | 174 | 0.70 | 0.88 | 27 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4777 Ų buried · 53 hydrogen bonds · protein-protein
- C–D · 4635 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 1048 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 411 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 210 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 4N0B · Crystal structure of Bacillus subtilis GabR, an autorepressor and transcriptional… · 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 C 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 4N0B · PDBe 4N0B · UniProt P94426
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