Research workbench
Crystal structure of the P115RHOGEF rgrgs domain in a complex with GALPHA(13):GALPHA(I1) chimera
Analyse Crystal structure of the P115RHOGEF rgrgs domain in a complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SHZ
- Type
- protein
- Length
- 1,037 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein GALPHA(13):GALPHA(I1) chimera; Rho guanine nucleotide…
- UniProt
- P10824, P27601, Q92888
- Ligands
- ALF, GDP, MG
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein GALPHA(13):GALPHA(I1) chimera | protein | 326 | 48% helix, 13% strand | P10824, P27601 |
| C | Rho guanine nucleotide exchange factor 1 | protein | 196 | 60% helix, 2% strand | Q92888 |
| D | Guanine nucleotide-binding protein GALPHA(13):GALPHA(I1) chimera | protein | 327 | 49% helix, 13% strand | P10824, P27601 |
| F | Rho guanine nucleotide exchange factor 1 | protein | 188 | 61% helix, 2% strand | Q92888 |
Ligands and binding sites
- ALF · Tetrafluoroaluminate ion · ligand · 2 copies · chains A, D
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 761 | 0.86 | 0.90 | 97 | empty |
| 2 | 388 | 0.81 | 0.91 | 66 | MG, ALF, GDP |
| 3 | 582 | 0.80 | 0.86 | 80 | MG, ALF, GDP |
| 4 | 280 | 0.73 | 0.86 | 46 | empty |
| 5 | 163 | 0.63 | 0.84 | 23 | empty |
Interfaces
6 interfaces between chains.
- D–F · 1493 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1473 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 621 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 554 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 429 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1SHZ · Crystal Structure of the p115RhoGEF rgRGS Domain in A Complex with Galpha(13):Galpha(i1)… · the same entry in another collection · chain A against A, TM-score 1.00
- P27601 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein subunit alpha-13… · a predicted model of the same protein · chain D against A, TM-score 0.98
- P10824 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain D against A, TM-score 0.95
- Q92888 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 1 (Q92888) · a predicted model of the same protein · chain F against A, TM-score 0.89
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 P10824
- Every structure of UniProt P27601
- Every structure of UniProt Q92888
- Elsewhere: RCSB PDB 1SHZ · PDBe 1SHZ · UniProt P10824 · UniProt P27601 · UniProt Q92888
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