MolNFT v1 · #36525 · protein
Benm effector-binding domain crystallized from high pH conditions
2F8D · Hth-type transcriptional regulator benm: “Benm effector-binding domain crystallized from high pH conditions”. X-ray diffraction, 2 ligands (BEZ, PO4), 5 pockets (best druggability 0.68). MolNFT v1 #36525 on GenesisL1: 3D structure…
- PDB
- 2F8D
- Type
- protein
- Length
- 439 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, PO4
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulator benm | protein | 221 | 35% helix, 27% strand | O68014 |
| B | Hth-type transcriptional regulator benm | protein | 218 | 35% helix, 28% strand | O68014 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 3 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.68 | 0.88 | 29 | empty |
| 2 | 246 | 0.67 | 0.84 | 34 | BEZ, GOL |
| 3 | 69 | 0.35 | 0.77 | 18 | empty |
| 4 | 51 | 0.30 | 0.76 | 18 | empty |
| 5 | 60 | 0.29 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1361 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 2F8D · BenM effector-Binding domain crystallized from high pH conditions · 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 0.98
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 O68014
- Elsewhere: RCSB PDB 2F8D · PDBe 2F8D · UniProt O68014
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