Research workbench
Benm effector binding domain with its effector benzoate
Analyse Benm effector binding domain with its effector benzoate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F78
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulator benm
- UniProt
- O68014
- Ligands
- BEZ
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulator benm | protein | 222 | 34% helix, 28% strand | O68014 |
| B | Hth-type transcriptional regulator benm | protein | 214 | 35% helix, 28% strand | O68014 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.70 | 0.83 | 35 | BEZ |
| 2 | 314 | 0.69 | 0.83 | 36 | BEZ |
| 3 | 82 | 0.53 | 0.85 | 19 | empty |
| 4 | 105 | 0.40 | 0.76 | 19 | BEZ |
| 5 | 123 | 0.38 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1344 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2F78 · BenM effector binding domain with its effector benzoate · the same entry in another collection · chain A against A, TM-score 1.00
- O68014 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator benm (O68014) · 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 O68014
- Elsewhere: RCSB PDB 2F78 · PDBe 2F78 · UniProt O68014
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