MolNFT v1 · #85213 · protein
Structural analyses of SLM1-pH domain demonstrate ligand binding in the non-canonical site
4A5K · Phosphatidylinositol 4,5-bisphosphate-binding protein slm 1: “Structural analyses of SLM1-pH domain demonstrate ligand binding in the non-canonical site”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.79). MolNFT…
- PDB
- 4A5K
- Type
- protein
- Length
- 458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate-binding protein slm 1
- UniProt
- P40485
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate-binding protein slm 1 | protein | 115 | 16% helix, 39% strand | P40485 |
| B | Phosphatidylinositol 4,5-bisphosphate-binding protein slm 1 | protein | 116 | 16% helix, 39% strand | P40485 |
| C | Phosphatidylinositol 4,5-bisphosphate-binding protein slm 1 | protein | 113 | 15% helix, 40% strand | P40485 |
| D | Phosphatidylinositol 4,5-bisphosphate-binding protein slm 1 | protein | 114 | 16% helix, 39% strand | P40485 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.79 | 0.81 | 114 | empty |
| 2 | 241 | 0.60 | 0.80 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 576 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 547 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 540 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 534 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4A5K · Structural analyses of Slm1-PH domain demonstrate ligand binding in the non-canonical site · the same entry in another collection · chain D against D, TM-score 1.00
- P40485 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 4,5-bisphosphate-binding… · a predicted model of the same protein · chain C against A, TM-score 0.87
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 P40485
- Elsewhere: RCSB PDB 4A5K · PDBe 4A5K · UniProt P40485
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