Research workbench
Crystal structure of SLM1-pH domain in complex with D-myo-inositol-4-phosphate
Analyse Crystal structure of SLM1-pH domain in complex with D-myo-inositol-4-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A6K
- Type
- protein
- Length
- 436 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1
- UniProt
- P40485
- Ligands
- I4D, PO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1 | protein | 110 | 15% helix, 40% strand | P40485 |
| B | Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1 | protein | 110 | 15% helix, 40% strand | P40485 |
| C | Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1 | protein | 109 | 17% helix, 40% strand | P40485 |
| D | Phosphatidylinositol 4,5-bisphosphate-binding protein SLM1 | protein | 107 | 17% helix, 41% strand | P40485 |
Ligands and binding sites
- I4D · D-myo-inositol-4-phosphate · ligand · 3 copies · chains A, B, C
- PO4 · Phosphate ion · ion · 7 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.64 | 0.83 | 28 | empty |
| 2 | 110 | 0.51 | 0.81 | 25 | empty |
| 3 | 78 | 0.35 | 0.76 | 15 | empty |
| 4 | 65 | 0.29 | 0.74 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–D · 929 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 830 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 457 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 337 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 308 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4A6K · Crystal structure of Slm1-PH domain in complex with D-myo-Inositol-4- phosphate · 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 D against A, TM-score 0.90
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 4A6K · PDBe 4A6K · UniProt P40485
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