MolNFT v1 · #31737 · protein
Crystal structure of the binding protein opuac in complex with proline betaine
2B4M · Glycine betaine-binding protein: “Crystal structure of the binding protein opuac in complex with proline betaine”. X-ray diffraction, 1 ligand (PBE), 4 pockets (best druggability 0.62). MolNFT v1 #31737 on GenesisL1: 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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