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Crystal structure of human G3BP1 in complex with semliki forest virus NSP3-25 comprising two fgdf motives
Analyse Crystal structure of human G3BP1 in complex with semliki forest virus NSP3-25… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FW5
- Type
- protein
- Length
- 293 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS GTPase-activating protein-binding protein 1; Non-structural protein 3
- EC
- 3.6.4.12, 3.6.4.13
- UniProt
- Q13283, P08411
- Ligands
- K, SO4
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS GTPase-activating protein-binding protein 1 (EC 3.6.4.12, 3.6.4.13) | protein | 139 | 30% helix, 40% strand | Q13283 |
| B | RAS GTPase-activating protein-binding protein 1 (EC 3.6.4.12, 3.6.4.13) | protein | 131 | 29% helix, 40% strand | Q13283 |
| C | Non-structural protein 3 | protein | 23 | 26% helix, 9% strand | P08411 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains B, A
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.57 | 0.90 | 21 | empty |
| 2 | 151 | 0.44 | 0.75 | 33 | empty |
| 3 | 75 | 0.36 | 0.76 | 14 | empty |
| 4 | 50 | 0.27 | 0.74 | 14 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1301 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 765 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5FW5 · Crystal structure of human G3BP1 in complex with Semliki Forest Virus nsP3-25 comprising… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13283 · AlphaFold monomer V2.0 prediction for RAS GTPase-activating protein- binding protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q13283
- Every structure of UniProt P08411
- Elsewhere: RCSB PDB 5FW5 · PDBe 5FW5 · UniProt Q13283 · UniProt P08411
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