Research workbench
Crystal structure of the binding protein opuac in complex with proline betaine
Analyse Crystal structure of the binding protein opuac in complex with proline betaine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2B4M
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine betaine-binding protein
- UniProt
- P46922
- Ligands
- PBE
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycine betaine-binding protein | protein | 264 | 41% helix, 23% strand | P46922 |
Ligands and binding sites
- PBE · 1,1-dimethyl-prolinium · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 286 | 0.62 | 0.80 | 44 | PBE |
| 2 | 163 | 0.61 | 0.83 | 30 | PBE |
| 3 | 57 | 0.35 | 0.78 | 17 | empty |
| 4 | 64 | 0.35 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 336 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2B4M · Crystal structure of the binding protein OpuAC in complex with proline betaine · the same entry in another collection · chain A against A, TM-score 1.00
- P46922 · AlphaFold monomer V2.0 prediction for glycine betaine-binding protein opuac (P46922) · 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 P46922
- Elsewhere: RCSB PDB 2B4M · PDBe 2B4M · UniProt P46922
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