Research workbench
Computationally-designed, modular SENSE/RESPONSE system (S3-2D)
Analyse Computationally-designed, modular SENSE/RESPONSE system (S3-2D) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OB5
- Type
- protein
- Length
- 1,026 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltodextrin-binding protein; Ankyrin repeat domain (ar), S3-2D variant
- UniProt
- A0A2Y0TBT9
- Ligands
- FPP, GLC
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Maltodextrin-binding protein | protein | 364 | 45% helix, 19% strand | A0A2Y0TBT9 |
| A | Maltodextrin-binding protein | protein | 360 | 45% helix, 20% strand | A0A2Y0TBT9 |
| C, D | Ankyrin repeat domain (ar), S3-2D variant | protein | 151 | 56% helix, 0% strand | — |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains B, D
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 377 | 0.76 | 0.85 | 31 | GLC |
| 2 | 353 | 0.73 | 0.84 | 32 | GLC |
| 3 | 452 | 0.72 | 0.82 | 44 | empty |
| 4 | 419 | 0.72 | 0.82 | 38 | FPP |
| 5 | 950 | 0.71 | 0.75 | 78 | empty |
Interfaces
3 interfaces between chains.
- A–C · 721 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 711 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 94 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6OB5 · Computationally-designed, modular sense/response system (S3-2D) · the same entry in another collection · chain B against B, 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
- Every structure of UniProt A0A2Y0TBT9
- Elsewhere: RCSB PDB 6OB5 · PDBe 6OB5 · UniProt A0A2Y0TBT9
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