MolNFT v1 · #57552 · protein
Crystal structure of P115RHOGEF rgs domain in complex with G alpha 13
3AB3 · Guanine nucleotide-binding protein G(K) subunit alpha…: “Crystal structure of P115RHOGEF rgs domain in complex with G alpha 13”. X-ray diffraction, 3 ligands (GDP, ALF, MG), 8 pockets (best druggability 0.80). MolNFT v1 #57552 on…
- PDB
- 3AB3
- Type
- protein
- Length
- 987 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(K) subunit alpha, guanine nucleotide-binding protein…
- UniProt
- Q9DC51, P27601, Q92888
- Ligands
- GDP, ALF, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(K) subunit alpha, guanine nucleotide-binding protein subunit alpha-13 | protein | 322 | 52% helix, 13% strand | Q9DC51, P27601 |
| B | Rho guanine nucleotide exchange factor 1 | protein | 182 | 62% helix, 0% strand | Q92888 |
| C | Guanine nucleotide-binding protein G(K) subunit alpha, guanine nucleotide-binding protein subunit alpha-13 | protein | 318 | 52% helix, 13% strand | Q9DC51, P27601 |
| D | Rho guanine nucleotide exchange factor 1 | protein | 165 | 68% helix, 0% strand | Q92888 |
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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.80 | 0.82 | 120 | MG, GDP, ALF |
| 2 | 642 | 0.78 | 0.84 | 80 | MG, GDP, ALF |
| 3 | 799 | 0.69 | 0.75 | 61 | empty |
| 4 | 289 | 0.68 | 0.83 | 28 | empty |
| 5 | 221 | 0.67 | 0.84 | 35 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1653 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1610 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 544 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 90 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3AB3 · Crystal structure of p115RhoGEF RGS domain in complex with G alpha 13 · 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 C against A, TM-score 0.99
- Q9DC51 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain C against A, TM-score 0.94
- Q92888 · AlphaFold monomer V2.0 prediction for rho guanine nucleotide exchange factor 1 (Q92888) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 Q9DC51
- Every structure of UniProt P27601
- Every structure of UniProt Q92888
- Elsewhere: RCSB PDB 3AB3 · PDBe 3AB3 · UniProt Q9DC51 · UniProt P27601 · UniProt Q92888
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