Research workbench
Simocycli C4 bound form of TetR-like repressor SimR
Analyse Simocycli C4 bound form of TetR-like repressor SimR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y31
- Type
- protein
- Length
- 474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Source
- STREPTOMYCES ANTIBIOTICUS
- Molecule
- Putative repressor SIMREG2
- UniProt
- Q9AMH9
- Ligands
- SMQ, CA, CL
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative repressor SIMREG2 | protein | 242 | 65% helix, 1% strand | Q9AMH9 |
| B | Putative repressor SIMREG2 | protein | 232 | 69% helix, 0% strand | Q9AMH9 |
Ligands and binding sites
- SMQ · Simocyclinone C4 · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
- CL · Chloride ion · ion · 8 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains A, B
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.85 | 0.87 | 71 | SMQ |
| 2 | 817 | 0.85 | 0.87 | 71 | SMQ |
| 3 | 239 | 0.67 | 0.84 | 28 | empty |
| 4 | 199 | 0.61 | 0.82 | 25 | empty |
| 5 | 85 | 0.35 | 0.76 | 19 | PG4 |
Interfaces
1 interface between chains.
- A–B · 3050 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 2Y31 · Simocyclinone C4 bound form of tetr-like repressor simr · 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
- Every structure of UniProt Q9AMH9
- Elsewhere: RCSB PDB 2Y31 · PDBe 2Y31 · UniProt Q9AMH9
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