Research workbench
Crystal structure of smggds-558 and farnesylated rhoa complex
Analyse Crystal structure of smggds-558 and farnesylated rhoa complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZHX
- Type
- protein
- Length
- 2,514 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAP1 GTPase-GDP dissociation stimulator 1; Transforming protein rhoa
- UniProt
- P52306, P61586
- Ligands
- FAR
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | RAP1 GTPase-GDP dissociation stimulator 1 | protein | 469 | 72% helix, 0% strand | P52306 |
| e, h | Transforming protein rhoa | protein | 163 | 32% helix, 20% strand | P61586 |
| f, g | Transforming protein rhoa | protein | 156 | 30% helix, 21% strand | P61586 |
Ligands and binding sites
- FAR · Farnesyl · ligand · 4 copies · chains A, e, B, f, C, g, D, h
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.83 | 0.97 | 29 | FAR |
| 2 | 935 | 0.82 | 0.83 | 89 | empty |
| 3 | 1156 | 0.81 | 0.83 | 126 | empty |
| 4 | 165 | 0.81 | 0.96 | 25 | FAR |
| 5 | 710 | 0.81 | 0.85 | 86 | empty |
Interfaces
17 interfaces between chains.
- B–f · 1848 Ų buried · 19 hydrogen bonds · protein-protein
- C–g · 1822 Ų buried · 20 hydrogen bonds · protein-protein
- D–h · 1759 Ų buried · 21 hydrogen bonds · protein-protein
- A–e · 1754 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 lipid (farnesylation).
Compared structures
- 5ZHX · Crystal structure of SmgGDS-558 and farnesylated RhoA complex · the same entry in another collection · chain h against h, TM-score 1.00
- P52306 · AlphaFold monomer V2.0 prediction for RAP1 GTPase-GDP dissociation stimulator 1 (P52306) · a predicted model of the same protein · chain A 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 P52306
- Every structure of UniProt P61586
- Elsewhere: RCSB PDB 5ZHX · PDBe 5ZHX · UniProt P52306 · UniProt P61586
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