Research workbench
Benm effector binding domain with its effector, CIS,CIS-muconate
Analyse Benm effector binding domain with its effector, CIS,CIS-muconate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F7A
- Type
- protein
- Length
- 441 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, CCU, SO4
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulator benm | protein | 228 | 32% helix, 26% strand | O68014 |
| B | Hth-type transcriptional regulator benm | protein | 213 | 34% helix, 28% strand | O68014 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- CCU · (2Z,4Z)-hexa-2,4-dienedioic acid · ligand · chains B
- SO4 · Sulfate ion · ion · chains B
- ACT · Acetate ion · additive · chains 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.68 | 0.82 | 36 | empty |
| 2 | 160 | 0.64 | 0.85 | 26 | CCU |
| 3 | 150 | 0.44 | 0.75 | 19 | empty |
| 4 | 86 | 0.43 | 0.79 | 12 | SO4 |
| 5 | 54 | 0.38 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1283 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2F7A · BenM effector binding domain with its effector, cis,cis-muconate · 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 2F7A · PDBe 2F7A · UniProt O68014
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