Research workbench
Complex of YPD1 and SLN1-R1 with bound MG2+ and BEF3-
Analyse Complex of YPD1 and SLN1-R1 with bound MG2+ and BEF3- in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R25
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphorelay intermediate protein YPD1; Osmosensing histidine protein kinase SLN1
- EC
- 2.7.13.3
- UniProt
- Q07688, P39928
- Ligands
- BEF, MG, NA
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphorelay intermediate protein YPD1 | protein | 166 | 62% helix, 0% strand | Q07688 |
| B | Osmosensing histidine protein kinase SLN1 (EC 2.7.13.3) | protein | 133 | 44% helix, 16% strand | P39928 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains A, B
- MG · Magnesium ion · metal · chains B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.37 | 0.76 | 32 | MG, BEF |
| 2 | 87 | 0.35 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 957 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2R25 · Complex of YPD1 and SLN1-R1 with bound Mg2+ and BeF3- · the same entry in another collection · chain A against A, TM-score 1.00
- Q07688 · AlphaFold monomer V2.0 prediction for phosphorelay intermediate protein YPD1 (Q07688) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P39928 · AlphaFold monomer V2.0 prediction for osmosensing histidine protein kinase SLN1 (P39928) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q07688
- Every structure of UniProt P39928
- Elsewhere: RCSB PDB 2R25 · PDBe 2R25 · UniProt Q07688 · UniProt P39928
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