Research workbench
Dreiklang - off state
Analyse Dreiklang - off state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ST3
- Type
- protein
- Length
- 698 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dreiklang
- Ligands
- WCR, PO4
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dreiklang | protein | 236 | 11% helix, 51% strand | — |
| B | Dreiklang | protein | 233 | 11% helix, 52% strand | — |
| C | Dreiklang | protein | 229 | 11% helix, 52% strand | — |
Ligands and binding sites
- WCR · [(2R,4Z)-2-(aminomethyl)-2-hydroxy-4-(4-hydroxybenzylidene)-5-oxoimidazolidin-1-yl]acetic acid · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 13 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.68 | 0.90 | 30 | PO4 |
| 2 | 598 | 0.67 | 0.77 | 59 | PO4 |
| 3 | 223 | 0.52 | 0.77 | 30 | PO4 |
| 4 | 73 | 0.51 | 0.85 | 16 | empty |
| 5 | 66 | 0.47 | 0.84 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1402 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 843 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 400 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 3ST3 · Dreiklang - off state · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 3ST3 · PDBe 3ST3
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