Research workbench
Crystal structure of the P-REX1 pH domain with inositol-(1,3,4,5)- tetrakisphosphate bound
Analyse Crystal structure of the P-REX1 pH domain with inositol-(1,3,4,5)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D3Y
- Type
- protein
- Length
- 272 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol 3,4,5-trisphosphate-dependent rac exchanger 1 protein
- UniProt
- Q8TCU6
- Ligands
- 4IP
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphatidylinositol 3,4,5-trisphosphate-dependent rac exchanger 1 protein | protein | 136 | 26% helix, 40% strand | Q8TCU6 |
Ligands and binding sites
- 4IP · Inositol-(1,3,4,5)-tetrakisphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.39 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 244 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5D3Y · Crystal Structure of the P-Rex1 PH domain with Inositol-(1,3,4,5)-Tetrakisphosphate Bound · the same entry in another collection · chain A against A, TM-score 1.00
- Q8TCU6 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 3,4,5-trisphosphate-dependent… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8TCU6
- Elsewhere: RCSB PDB 5D3Y · PDBe 5D3Y · UniProt Q8TCU6
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