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Structure of the pleckstrin homology domain from GRP1 in complex with inositol 1,3,4,5-tetrakisphosphate
Analyse Structure of the pleckstrin homology domain from GRP1 in complex with inositol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FHX
- Type
- protein
- Length
- 249 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide exchange factor and integrin binding protein homolog GRP1
- UniProt
- O08967
- Ligands
- 4IP, SO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 13% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide exchange factor and integrin binding protein homolog GRP1 | protein | 123 | 15% helix, 37% strand | O08967 |
| B | Guanine nucleotide exchange factor and integrin binding protein homolog GRP1 | protein | 126 | 11% helix, 37% strand | O08967 |
Ligands and binding sites
- 4IP · Inositol-(1,3,4,5)-tetrakisphosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.64 | 0.93 | 19 | SO4 |
| 2 | 92 | 0.48 | 0.82 | 22 | empty |
| 3 | 165 | 0.47 | 0.76 | 27 | empty |
| 4 | 103 | 0.45 | 0.79 | 20 | 4IP |
| 5 | 100 | 0.45 | 0.79 | 17 | 4IP |
Interfaces
1 interface between chains.
- A–B · 1217 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 1FHX · Structure of the pleckstrin homology domain from GRP1 in complex with inositol… · the same entry in another collection · chain A against A, TM-score 1.00
- O08967 · AlphaFold monomer V2.0 prediction for cytohesin-3 (O08967) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 O08967
- Elsewhere: RCSB PDB 1FHX · PDBe 1FHX · UniProt O08967
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