Research workbench
Crystal structure of the effector binding domain of a benm variant (R156H,T157S)
Analyse Crystal structure of the effector binding domain of a benm variant (R156H,T157S) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H99
- Type
- protein
- Length
- 432 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional regulator benm
- UniProt
- O68014
- Ligands
- SO4, CL
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional regulator benm | protein | 215 | 34% helix, 29% strand | O68014 |
| B | Hth-type transcriptional regulator benm | protein | 217 | 34% helix, 29% strand | O68014 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- CL · Chloride ion · ion · chains B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- GOL · Glycerol · additive · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.62 | 0.85 | 31 | ACT |
| 2 | 117 | 0.46 | 0.78 | 24 | SO4, CL |
| 3 | 105 | 0.36 | 0.74 | 23 | empty |
| 4 | 55 | 0.30 | 0.76 | 14 | empty |
| 5 | 61 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1278 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2H99 · Crystal structure of the effector binding domain of a BenM variant (R156H,T157S) · 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 A 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 2H99 · PDBe 2H99 · UniProt O68014
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