Research workbench
Crystal structure of galphaq in complex with full-length human PLCBETA3
Analyse Crystal structure of galphaq in complex with full-length human PLCBETA3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GNK
- Type
- protein
- Length
- 2,428 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(Q) subunit alpha; 1-phosphatidylinositol…
- EC
- 3.1.4.11
- UniProt
- P21279, Q01970
- Ligands
- GDP, ALF, MG, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(Q) subunit alpha | protein | 337 | 50% helix, 13% strand | P21279 |
| B | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 (EC 3.1.4.11) | protein | 769 | 32% helix, 22% strand | Q01970 |
| C | Guanine nucleotide-binding protein G(Q) subunit alpha | protein | 321 | 49% helix, 13% strand | P21279 |
| D | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 (EC 3.1.4.11) | protein | 766 | 32% helix, 22% strand | Q01970 |
| E | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 | protein | 235 | 86% helix, 0% strand | Q01970 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, C
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CA · Calcium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 940 | 0.79 | 0.81 | 68 | empty |
| 2 | 1166 | 0.77 | 0.79 | 72 | empty |
| 3 | 269 | 0.77 | 0.89 | 26 | empty |
| 4 | 265 | 0.76 | 0.89 | 26 | empty |
| 5 | 239 | 0.75 | 0.90 | 42 | GDP, ALF, MG |
Interfaces
4 interfaces between chains.
- A–B · 1682 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1644 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1005 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 407 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4GNK · Crystal structure of Galphaq in complex with full-length human PLCbeta3 · the same entry in another collection · chain E against E, TM-score 1.00
- Q01970 · AlphaFold monomer V2.0 prediction for 1-phosphatidylinositol 4,5-bisphosphate… · a predicted model of the same protein · chain B against A, TM-score 0.99
- P21279 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(Q) subunit… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P21279
- Every structure of UniProt Q01970
- Elsewhere: RCSB PDB 4GNK · PDBe 4GNK · UniProt P21279 · UniProt Q01970
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