Research workbench
Crystal structure of RGD1P F-bar domain in complex with inositol phosphate
Analyse Crystal structure of RGD1P F-bar domain in complex with inositol phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WPC
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rho GTPase-activating protein RGD1
- UniProt
- P38339
- Ligands
- IHP
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rho GTPase-activating protein RGD1 | protein | 283 | 82% helix, 0% strand | P38339 |
| B | Rho GTPase-activating protein RGD1 | protein | 288 | 77% helix, 0% strand | P38339 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.79 | 0.97 | 26 | empty |
| 2 | 147 | 0.58 | 0.83 | 25 | empty |
| 3 | 51 | 0.44 | 0.83 | 15 | empty |
| 4 | 76 | 0.43 | 0.79 | 19 | empty |
| 5 | 65 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 4499 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4WPC · Crystal structure of Rgd1p F-BAR domain in complex with inositol phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- P38339 · AlphaFold monomer V2.0 prediction for rho GTPase-activating protein RGD1 (P38339) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P38339
- Elsewhere: RCSB PDB 4WPC · PDBe 4WPC · UniProt P38339
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