Research workbench
Crystal structure of the GDP-bound RAB1A S25N mutant in complex with the coiled-coil domain of lida from legionella pneumophila
Analyse Crystal structure of the GDP-bound RAB1A S25N mutant in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SFV
- Type
- protein
- Length
- 521 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rab-1A; Lida protein, substrate of the DOT/ICM system
- UniProt
- P62820, A5IFX1
- Ligands
- GDP
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rab-1A | protein | 179 | 34% helix, 24% strand | P62820 |
| B | Lida protein, substrate of the DOT/ICM system | protein | 342 | 63% helix, 16% strand | A5IFX1 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.82 | 0.83 | 92 | GDP |
| 2 | 1061 | 0.75 | 0.78 | 92 | empty |
| 3 | 148 | 0.50 | 0.78 | 22 | empty |
| 4 | 156 | 0.50 | 0.78 | 22 | empty |
| 5 | 112 | 0.40 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2195 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 3SFV · Crystal structure of the GDP-bound Rab1a S25N mutant in complex with the coiled-coil… · the same entry in another collection · chain A against A, TM-score 1.00
- P62820 · AlphaFold monomer V2.0 prediction for RAS-related protein rab-1A (P62820) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P62820
- Every structure of UniProt A5IFX1
- Elsewhere: RCSB PDB 3SFV · PDBe 3SFV · UniProt P62820 · UniProt A5IFX1
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