MolNFT v1 · #60089 · protein
The compatible solute-binding protein opuac from bacillus subtilis in complex with dmsa
3CHG · Glycine betaine-binding protein: “The compatible solute-binding protein opuac from bacillus subtilis in complex with dmsa”. X-ray diffraction, 1 ligand (313), 9 pockets (best druggability 0.85). MolNFT v1 #60089 on GenesisL1: 3D…
- PDB
- 3CHG
- Type
- protein
- Length
- 1,031 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine betaine-binding protein
- UniProt
- P46922
- Ligands
- 313
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Glycine betaine-binding protein | protein | 257 | 35% helix, 18% strand | P46922 |
| A, B, C | Glycine betaine-binding protein | protein | 258 | 39% helix, 22% strand | P46922 |
Ligands and binding sites
- 313 · (dimethyl-lambda~4~-sulfanyl)acetic acid · ligand · 4 copies · chains D, B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.85 | 0.87 | 97 | empty |
| 2 | 355 | 0.75 | 0.86 | 48 | empty |
| 3 | 388 | 0.72 | 0.83 | 33 | empty |
| 4 | 116 | 0.59 | 0.85 | 18 | empty |
| 5 | 104 | 0.53 | 0.83 | 18 | empty |
Interfaces
5 interfaces between chains.
- D–B · 705 Ų buried · 6 hydrogen bonds · protein-protein
- D–A · 590 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 530 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 494 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 481 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3CHG · The compatible solute-binding protein OpuAC from Bacillus subtilis in complex with DMSA · the same entry in another collection · chain B against B, 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 D against A, TM-score 0.99
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 3CHG · PDBe 3CHG · UniProt P46922
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